Thursday, April 28, 2016

Fun and games with Otangelo Grasso about photosynthesis

Otangelo Grasso just posted another one of his screeds. This time it's on photosynthesis. All of his "essays' conform to the same pattern. He looks for some complex set of biochemical reactions, usually in complex animals, then claims that it couldn't possibly have evolved because the whole thing is irreducibly complex according to his understanding of biochemistry and evolution.

It's a classic argument from ignorance.

In this case it's photosynthesis in flowering plants. He posted this figure from the Kegg database ....


Then he says,
In photosynthesis , 26 protein complexes and enzymes are required to go through the light and light independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose as end product , a metabolic intermediate for cell respiration. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is a interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage, all happened by a series of natural events that we can call ad hoc mistake "formed in one particular moment without ability to consider any application." , to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to " feed " ATP synthase nano motors to produce ATP , and so on ? Such independent structures would have not aided survival. Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning, various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.
I responded on Facebook, pointing out that the cytochrome bc complex and ATP synthase pre-date photosynthesis [Facebook: Photosynthesis]. I also pointed out that there are many living species that use only simpler versions of photsystem I or only photosystem II to carry out photosynthesis [e.g. A Simple Version of Photosynthesis]. Those nasty little facts don't seem to fit with his claim that, "In these systems, nothing works until all the necessary components are present and working."

I probably should have known better. Otangelo Grasso's standard response to such criticism is to avoid dealing directly with his false statements and shift the goalposts on to some other topic. He then posts all kinds of links to websites that seem to back up his claims even if they have nothing to do with the criticisms. You can see him at work on the Facebook thread.

It's pretty frustrating. I probably shouldn't respond to kooks, especially those who think they are experts in biochemistry.


274 comments :

  1. Well, that comment thread was rather painful! This guy seems like a good example of "knowing" enough to be dangerous.

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  2. Your responding to kooks who think they know biochemistry is probably helpful to some of the readers, though of course not to the kooks.

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  3. Larry

    as Behe said: In order to say that some function is understood, every relevant step in the process must be elucidated. My last comment and answer at FB was: Whatever photosynthetic system you come up with, which you entitle as the most simple and basic one, which also keeps the Basic function , is Irreducibly complex.

    Lets keep in mind how IC is defined ( there are 4 very similar formulations, i will highlight Dembskis one ) :

    William Dembski's Enhanced Definition — "A system performing a given BASIC FUNCTION is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system." (No Free Lunch, page 285, 2001)

    Robert Blankenship, professor of biochemistry at Arizona State University , and expert on photosynthesis, openly admits:

    “The process of photosynthesis is a very complex set of INTERDEPENDENT metabolic pathways. How it could have evolved is a bit mysterious.”

    In the scientific paper: Evolutionary Relationships Among Photosynthetic Bacteria, Firmicutes (Heliobacterium) are indicated to be earliest branching photosynthetic bacteria.

    You mention that it could have co-opted cytochrome bc is entirely irrelevant, as Behe states :

    http://reasonandscience.heavenforum.org/t1572-irreducible-complexity-is-an-obstacle-to-darwinism-even-if-parts-of-a-system-have-other-functions

    I never wrote that individual parts of an IC system couldn't be used for any other purpose. (That would be silly—who would ever claim that a part of a mousetrap couldn't be used as a paperweight, or a decoration, or a blunt weapon?) Quite the opposite, I clearly wrote in Darwin's Black Box that even if the individual parts had their own functions, that still does not account for the irreducible complexity of the system. In fact, it would most likely exacerbate the problem, as I stated when considering whether parts lying around a garage could be used to make a mousetrap without intelligent intervention.

    Not only is photosynthesis a interdependent system, but the single protein complexes are also irreducible complex, and so is the assembly and biosynthesis pathway. A example i have made a indepth study is the biosynthesis pathway of Chlorophyll a, which i will provide evidence that the pathway is IC in the next post.

    more about evolution of photosynthesis:

    http://reasonandscience.heavenforum.org/t1545-origin-and-evolution-of-photosynthesis

    ReplyDelete
    Replies
    1. You said, "Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately?"

      Do you still believe that a membrane-associated electron transport chain (i.e. the cytochrome bc complex) cannot exist and be functional without an accompanying photosystem I or II?

      Do you still believe that it is impossible to have photosynthesis without an oxygen evolving complex?

      Do not try and change the subject. Answer my questions. Do you or do you not stand by the original statements you made?

      Also, you are confused about the distinction between irreducible complexity. Just because something is irreducibly complex by some strict definition doesn't mean it could not have evolved. It's true that today if you remove any of the important proteins in the system you showed, it would not function. It's not true that this is proof it could never heave arisen by natural means.

      Delete
    2. The cytochrome bc complex is used in mitochondria, while cytochrome b6f in photosynthesis. What is your point ? Because cytochrome is used in other biological systems, photosynthesis is not IC ? That is a irrelevant, invalid, argument, as already explained. Even in the supposed primordial photosynthesis mechanism in Heliobacterium modesticaldum, cytochrome bc is indispensable and irreducible, if removed, photosynthesis ceases to function. So in various versions, its a indispensable protein complex. And even if it could have been co-opted from another biological system,

      For a working biological system to be built by exaptation , the five following conditions would all have to be met:

      C1: Availability. Among the parts available for recruitment to form the system, there would need to be ones capable of performing the highly specialized tasks of individual parts, even though all of these items serve some other function or no function.

      C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

      C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

      C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a system are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

      C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if sub systems or parts are put together in the right order, they also need to interface correctly.

      ( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

      In regard of your second question:

      Do you still believe that it is impossible to have photosynthesis without an oxygen evolving complex?

      By asking this, you ignore what i wrote above, namely: Whatever photosynthetic system you come up with, which you entitle as the most simple and basic one, which also keeps the basic function , is Irreducibly complex.

      Are you wilfullingly making obtuse and irrelevant questions in regard of my points raised ? Are you actually interested to find out what explanation of the origin of photosynthesis makes most sense, or are you just concerned to try to debunk my claims, and protect your holy cow, evolution , from being sacrificed ?

      Delete
    3. Stupid man can't figure out that IC systems can be produced by natural processes even after being told twice. Must talk to stupid man slow and simple. Make cave man understand.

      Consider natural arch. If man remove piece of arch, arch break. Arch is IC. Arch have function: mammoth use arch cross river. Same as bridge man make. How arch form? Sediment collect on soft rock. Sediment get harder. Now has more pieces than it need. If man remove part, system not break. System redundant.

      Then big river come. River erode soft rock below, leave hard rock above. Make natural arch. Mammoth use as bridge. If man remove big part, bridge collapse.

      Natural process make it. Great Spirit not needed. High Priest say Great Spirit make arch. Him shake bones, say Great Spirit want him have all women and mammoth meat. Me think mammoth stepped on head when baby.

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    4. oh look. Needs to resort to name calling to make a point. Sad.

      Here some basic rules. Hope this helps.

      If you want to win a debate with a proponent of intelligent design like me, here a suggestion :

      Do not :
      try to attack my knowledge
      Nor my education, or ask for my credentials
      Nor my source.
      Neither argue that the argument is from ignorance ( its not )
      nor argue its pseudo science ( my arguments are usually very detailled. Pseudo-science is the oposit )
      Nor attack the bible ( intelligent has nothing to do with the bible )
      nor make any explitic adhom ( it adds nothing to your case, nor does it make naturalism more true )
      nor acuse me of being biased ( we are all to a certain degree. You too )
      nor call my inference magic ( A potent and intelligent cause makes still more sense than everything coming from nothing )
      or suggest to peer review it ( the hostility of the scientific establishment towards intelligent design is well known )
      nor acuse me or my source of lying ( unless you have proof of it, then point out exactly why its a lie )

      What to do:
      1.Study if the premise is true. Take your time to actually understand what is presented to you.
      2. Analyse if a compelling case through naturalism exists
      3. Analyse if intelligent design is not a better explanation
      4. If you think , naturalism has better explanatory power, refute claims of ID proponents, and listen to their defense, or
      5. Admit ID has the better explanatory power, and check if that is the case in regard of other issues as well.
      6. If various issues are better explained through ID, change your world view.

      As to your arch example. Old tiresome boring arguments. Nothing new.

      In "Complexity by Subtraction," they argue that rather than being built up as normally imagined by Darwinists, from simple to complex, evolution may happen the opposite way. Starting out with something highly complex, there follows a loss of complexity, and you end up with an evolutionary product that is simpler and more streamlined. Where did you get the highly complex beginning? That must remain the usual free gift. From the Abstract:

      The standard [Darwinian] thinking could be right, even in general. But alternatives have not been much discussed or investigated, and the possibility remains open that other routes may not only exist but may be the norm. Our purpose here is to introduce a new route to functional complexity, a route in which complexity starts high, rising perhaps on account of the spontaneous tendency for parts to differentiate. Then, driven by selection for effective and efficient function, complexity decreases over time. Eventually, the result is a system that is highly functional and retains considerable residual complexity, enough to impress us.

      The problem is always explaining how biological information or function is built up in the first place.

      Instead of emerging by gradually and incrementally adding new genes, cells, tissues or organs over time, what if some so-called "irreducibly complex" structures came to be by gradually losing parts, becoming simpler and more streamlined? Think of naturally occurring rock arches, which start as cliffs or piles of stone and form when bits of stone are weathered away. They call the principle "complexity by subtraction."

      This is all very revealing. In the geological context, we know very well how, as a starting point, "cliffs or piles of stone" form. It's readily comprehensible how, worn by water or weather, an arch may appear. In the biological context, we do not know how the starting point -- functioning "genes, cells, tissues or organs" -- got there.

      http://reasonandscience.heavenforum.org/t2254-does-the-mullerian-two-step-proposal-refute-irreducible-complexity

      Delete
    5. "try to attack my knowledge" - So we should just accept all your "knowledge" is right? What did you even mean by this?

      "Nor my education, or ask for my credentials " -Yea, because those are not important at all, right? There is not even a slight possibility that it is exactly your lack of education and credentials that is causing your confusion, right?

      "Nor my source. " - So what, you can make any sort of claim and you dont have to support it at all?

      "Neither argue that the argument is from ignorance ( its not ) " - Oh wow. So you magically know that you will never make a faulty argument in your life. Amazing.

      "nor argue its pseudo science ( my arguments are usually very detailled. Pseudo-science is the oposit ) " - What does the level of detail have to do with something being pseudoscience? I have seen some really detailed works about natal charts, that does not make them right.

      "Nor attack the bible ( intelligent has nothing to do with the bible ) " - Yeeea.

      "nor make any explitic adhom ( it adds nothing to your case, nor does it make naturalism more true ) " - Actual ad hominems are rare. I have yet to see a single one here.

      "nor acuse me of being biased ( we are all to a certain degree. You too ) " - There is a difference between being biased by various things. For example, Larry might be biased in favour of drift since that is what he focuses on. This is hugely different from being biased by your religion views.

      "nor call my inference magic ( A potent and intelligent cause makes still more sense than everything coming from nothing ) " - What is wrong with calling it magic? It is magic by any definition of magic I can think of. A supernatural explanation never makes more sense than saying that we dont know.

      "or suggest to peer review it ( the hostility of the scientific establishment towards intelligent design is well known ) " - The hostility of the scientific establishment to total nonsense is know. I have yet to read a single paper by the Id crowd that i personally also would not completely reject for obvious scientific reasons.

      "nor acuse me or my source of lying ( unless you have proof of it, then point out exactly why its a lie )" - The first somewhat rational criteria.

      Delete
    6. I think "intelligent has nothing to do with the bible" is my new favourite creationist quote.

      Delete
  4. The German biologist Hoimar von Ditfurth makes this comment on the complex structure of so-called "primitive" algae:

    The oldest fossils so far discovered are objects fossilized in minerals which belong to blue green algae, more than 3 billion years old. No matter how primitive they are, they still represent rather complicated and expertly organized forms of life

    It looks like photosynthesis as a process is quite old.

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    Replies
    1. But, where & how did photosynthesis occur? Does Darwinism have an answer?

      Delete
    2. @Bill Cole

      Nobody believes that photosynthetic bacteria are that ancient. The "blue green algae" are cynaobacteria. Their dual photosystems clearly evolved late from a combination of a type I reaction center in species like Heliobacter and green sulfur bacteria and a type II reaction center from species like purple bacteria and green filamentous bacteria.

      The oxygen evolving complex was a late addition.

      All phylogenetic trees show photosynthetic bacteria arising late in prokaryotic evolution—probably not until 500-1000 million years after the first living cells.

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    3. von Dittfurt was (he died long ago) a medical doctor & popular science writer who wrote in the 1970ties and 1980ties on science.
      I liked his writing when I was 16. To call him an authority on photosythesis is an exaggeration.

      Delete
    4. @Larry: Even later than that. Living cells were around for at least 3.8Ga, with some evidence pointing to over 4Ga. Early photosynthetic activity produced the banded iron formations, which range back 2.5Ga. That means that the time between first cellular life and photosynthesis is at least 1.3Ga, possibly even as much as 1.6Ga.

      Molecular clock dating of early splits is highly problematic, because fossil calibrations using only outgroups are often unreliable (although there are cases where in-group fossils don't have a notable effect on dates). It's worth noting that geobiochemicla approaches may help resolve this issue, because in some cases you can pinpoint some compound in rocks (after diagenetic alteration) to some biochemical pathway.

      Delete
  5. Larry wrote:

    "...I also pointed out that there are many living species that use only simpler versions of photsystem I or only photosystem II to carry out photosynthesis [e.g. A Simple Version of Photosynthesis]. Those nasty little facts don't seem to fit with his claim that, "In these systems, nothing works until all the necessary components are present and working."

    Larry,
    I'm not being disrespectful here but...

    Just because other species use a "simpler version of photogenesis system"-I would call them the super-efficient enough for the particular species-it doesn't mean that "more complex" photogenesis versions evolved from the "simpler" ones, well, unless you have scientific proof of that... You don't!

    To make a claim you are making, you absolutely need to provide the missing evidence of the transition between the two unrelated systems, and between two totally different species, which I emphasize that I know you don't have. How is that science Larry?

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    Replies
    1. Otangelo Grasso made the claim that they absolutely could not have evolved because all the systems needed to be in place or nothing would work. I showed examples of simpler systems that work just fine.

      To make the claim he was making he absolutely needed to provide evidence which I know he doesn't have. How is that science, Eric?

      You seem to be rather selective in your criticisms. Why is that?

      Delete
    2. Larry does not need photos of every intermediate step to refute claims of IC. If you call something irreducibly complex and we point to a reduced form that is functional, it's not irreducible. Full stop.

      It is not necessary to present photos of the reduced form turning into the alleged IC structure. It could even go the other way, the alleged IC structure could be the parent of the reduced form, or they could be cousins, or $%&#ing Tolkien Elves could have made the reduced form. It...doesn't...matter... who made it. Or when it was made. Or if it were made in Santa's workshop on the North Pole. Does. Not. Matter.

      If it exists in reduced form anywhere, anytime, and has any function, it ain't irreducible, and YOU. WERE. WRONG.

      And if it were irreducible, so what? We know natural processes make IC structures. That's another discussion.

      Delete
    3. "Otangelo Grasso made the claim that they absolutely could not have evolved because all the systems needed to be in place or nothing would work. I showed examples of simpler systems that work just fine."

      As a matter of principle, just because "simpler systems" exist and work well in other, unrelated organisms, it doesn't mean that those system evolved into more complex ones by evolutionary-Darwinian means-in another, unrelated organisms. How do you explain that Larry?

      To prove your point Larry, you would have to do a lot of work and break many established evolutionary rules.

      You would also have experimentally demonstrate either that the "simpler system" can evolve into the more complex one in small steps-or whatever the Darwinists preach today. Or that the complex system can compensate when one of the functioning parts of the systems is removed or disabled.

      Can you do that?

      None of that has been done so far, so Grasso can very well make the same claims you do, which both of you call science;

      He claims that if you stick to the Darwinian ideology, even the modern one, you can't claim that the complex system evolved by those means from simpler ones.
      That's Grasso's science. I have to agree.

      To make the claim he was making he absolutely needed to provide evidence which I know he doesn't have. How is that science, Eric?

      Neither do you Larry have provide any evidence, not to mentions scientific or experimental.

      So, in order for your claim to be scientific, you should AT LEAST provide examples of some intermediate but still functioning systems between the "simple systems" and the complex ones, though unrelated organisms.

      Otherwise, your claim has no merit whatsoever ever since you have brought "the real science" into the picture.

      You seem to be rather selective in your criticisms. Why is that?

      Maybe, but the true science should have no problem defending itself, don't you think Larry? That's is the beauty of trues science, or it should be actually...The goal of true science should be to search for the truth and not to support preconceived ideas, shouldn't it?

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    4. "He claims that if you stick to the Darwinian ideology, even the modern one, you can't claim that the complex system evolved by those means from simpler ones.
      That's Grasso's science. I have to agree."


      Me too. That's Grasso's "science". I agree.

      Delete
    5. What do you know besides your ideology?

      I have 100 questions for you to prove your beliefs. If you provide scientific or reasonable evidence for 1o of those questions, you can pass.

      Are you interested?

      Delete
    6. What are my beliefs? Shouldn't you be asking me what I believe, rather than proof for it? You seem to think you have a clue about what beliefs I hold. In all likelihood you don't.

      You've made me curious though. Please tell me what you think I believe.

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    7. Diogenes,

      I have written the response to Larry's post before seeing your post first. I don't know how it happened.

      What struck me though is that you had already predicted where I was going to strike.

      Good for you! You have proven again, at least to me, that you are not stupid at all. Too bad that your great incite is so selective... It won't last though, unless you deny yourself...

      Delete
    8. Eric,
      "None of that has been done so far, so Grasso can very well make the same claims you do, which both of you call science; "

      So you argument amounts to nothing more than neither side has step by step evidence for the pathways of photosynthesis that we see today, so either explanation is equally likely. That's not much help.

      Delete
    9. Irreducible Complexity according to the modern evolutionary theory.

      Larry and others claim that photosynthesis in flowering plants is NOT irreducibly complex;

      meaning if one part of the whole photosynthesis system is missing or is dysfunctional, the whole system is irreducibly complex because it can't function without it. Therefore, the conclusion is that it could not have evolved by Darwinian means...more or less.

      However, Larry and others claim that a "simpler system" is functioning in other, unrelated organism, therefore the more complex photosynthesis system in flowering plants is not irreducibly complex because of the simpler system that works somewhere else.

      Is this true? Could the photosynthesis system in flowering plants evolved from other "simpler" systems in unrelated organisms?

      Let's see...

      Let's use an analogy of a mechanical broom street sweeper- to depict photosynthesis in flowering plants

      and hand street broom-to depict the simpler system functioning in other organisms:

      hand brooms: http://www.cepial.eu/en/manual_street_cleaning/brooms_brushesForStreetSweepers.html

      According to Larry's claim and others, the mechanical broom street sweeper is not irreducibly complex because there are much simpler systems (Diogenes used the word cousins) that just funtion fine, therefore the much complex mechanical broom street sweepers are not irreducibly complex.

      It may look fine on the picture but the real problem is that those complex mechanical boom street sweepers had to have evolved from those simpler hand brooms to make the theory plausible.

      But there is an obvious problem for anyone who applies logic to this claim. How did the simpler hand brooms evolved into complex machines-whatever the mechanism is? How?

      Everyone applying logic can see that there is a serious problem to this way of thinking; for a hand broom to evolve into a mechanical street broom sweeper you need more materials, parts and an assembly line just like here:

      https://www.youtube.com/watch?v=4kjruGYv_eI


      Evolution unrealistic enthusiasts seem to forget the most important part...

      Delete
    10. Larry and others claim that photosynthesis in flowering plants is NOT irreducibly complex; meaning if one part of the whole photosynthesis system is missing or is dysfunctional, the whole system is irreducibly complex because it can't function without it.

      I claim that the flowering plant photosynthesis system IS irreducibly complex but we have a perfectly good explanation of how it evolved from simpler systems. IDiots are the only people who claim that irreducibly complex systems can't arise by natural means (e.g. evolution). Try and keep up.

      Eric, your inability to follow a simple train of logic and your persistent rejection of scientific facts is becoming tedious.

      Shape up or find another blog to spam.

      Delete
    11. This topic should better have the title: Fun and games of Otangelo Grasso with Laurence A. Moran

      Larry wrote :

      I claim that the flowering plant photosynthesis system IS irreducibly complex but we have a perfectly good explanation of how it evolved from simpler systems.

      It seems you are ignorant of the very basic fact that a irreducible complexs system cannot evolve BY DEFINITION ( Mikkel despite of have being schooled of this several times has yet to learn it ) :

      Michael Behe's "Evolutionary" Definition — "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." (A Response to Critics of Darwin's Black Box, 2002)

      An irreducibly complex system cannot be produced gradually by slight, successive modifications of a precursor system, since any precursor to an irreducibly complex system is by definition nonfunctional. Since natural selection requires a function to select, an irreducibly complex biological system, if there is such a thing, would have to arise as an integrated unit for natural selection to have anything to act on. It is almost universally conceded that such a sudden event would be irreconcilable with the gradualism Darwin envisioned."In the quote above, Behe notes that there is a fundamental quality of any irreducibly complex system in that, "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.” Behe elaborates upon this definition saying"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway."

      Delete
    12. Larry wrote: I claim : we have a perfectly good explanation of how it evolved from simpler systems.

      Here either

      a) you are uniformed in regard of the status quo and real situation of scientific knowledge of the origin of photosynthesis

      or

      b) you have hidden knowledge not yet known by anyone else of how photosynthesis evolved. If that is the case, please share it with us ( eagerly waiting )

      or

      c) you are lying.

      “The process of photosynthesis is a very complex set of interdependent metabolic pathways “How it could have evolved is a bit mysterious.”
      Robert Blankenship, professor of biochemistry at Arizona State University

      The origin of the oxygen evolving complex ( OEC ) is an enigma.
      Oxygen evolving complex in Photosystem II: Better than excellent Mohammad Mahdi Najafpour*a and Govindjeeb

      Deep in the heart of this nest of proteins lies the manganese cluster, whose precise arrangement of atoms remains one of biology's outstanding problems.
      One of the outstanding questions concerning the early Earth is how ancient phototrophs made the evolutionary transition from anoxygenic to oxygenic photosynthesis, which resulted in a substantial increase in the amount of oxygen in the atmosphere.
      Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers, James P. Allen

      Perhaps the most widely discussed yet poorly understood event in the evolution of photosynthesis is the invention of the ability to use water as an electron donor, producing O2 as a waste product and giving rise to what is now called oxygenic photosynthesis.
      Transition from Anoxygenic to Oxygenic Photosynthesis in a Microcoleus chthonoplastes Cyanobacterial Mat. Jørgensen BB1, Cohen Y, Revsbech NP.

      ......and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits
      Complex evolution of photosynthesis. Xiong J1, Bauer CE.

      While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved.
      Manganese-oxidizing photosynthesis before the rise of cyanobacteria Jena E. Johnsona, Samuel M. Webbb

      Early Evolution of Photosynthesis1 Robert E. Blankenship

      To understand the origin and early evolution of photosynthesis, we need to consider mechanisms and evolution of all these subsystems and processes:

      Evolutionary origins of oxygen evolution center and linked photosystems are important unsolved problems.
      Pigments ( Chls , carotenoids, bilins )
      Reaction centers (including O2 Evolution Center)
      Antenna complexes
      Electron transfer pathways
      Carbon fixation pathways
      Photoprotection mechanisms
      Integration into cellular metabolism
      No single branching diagram can represent the complex path of evolution of photosynthesis.
      The evolution of PS2 proteins has been partially by gene recruitment and partially by gene duplication, but most of the proteins are orphans, with no known source.

      Origin and Evolution of Photosynthesis- Remaining Challenges

      Nature of the earliest PS systems not known
      Significance of gene duplications in RC evolution not understood
      Evolutionary origin of the oxygen evolving complex not known
      No good understanding of how two photosystems were linked in series

      Delete
    13. An irreducibly complex system cannot be produced gradually by slight, successive modifications of a precursor system, since any precursor to an irreducibly complex system is by definition nonfunctional.

      You seem unfamiliar with the concept of "circular reasoning. Would you like me to explain that for you?

      Delete
    14. @Otangelo Grasso

      Another possibility is ...

      d) I have the same kind of knowledge available to anyone who takes the time to investigate with an open mind. You lack this knowledge, which is why you make arguments from ignorance.

      Delete
    15. Larry

      if what you say is true, following are the possibilites:

      a) the authors of the papers i cited are either suffering of collective cognitive dissonance, or are terribly out of date with their information, and newer scientific results are available , which i surprisingly have not found anywhere over the web, or they are making false claims , and these claimes were not noted through the peer review process

      b) you are right. In that case you should have already presented the recent papers which provide compelling naturalistic explanations about how photosynthesis came to be.

      c) they are right, and you conveniently show one more time wilful ignorance of the scientific data that you have taken knowledge of, and behave as it were nonexistent.

      But taking your trackrecord into consideration, its evident that c is true.

      Thanks for playing......

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    16. Otangelo Grasso,

      Concerning a),

      Which of those authors claim naturalistic explanations cannot show how photosynthesis came to be? They all claim that the evolution of these systems are unresolved, and that we don't know for certain how they evolved. In c) you assume they were all arguing that naturalistic explanations for photosynthesis are impossible, but they actually claim that they just don't know.

      Delete
    17. When methodological naturalism is applied, the only explanation for the origin of photosynthesis is evolution. Larry claims like a mantra: we have a perfectly good explanation of how it evolved from simpler systems.. If that were the case, there would exist far more convincing , clear scientific answers and explanations. This is far from being the case. Based on scientific papers, quite a different picture arises. Instead of compelling answers, questionmarks and lack of understanding, generalized ignorance, and conceptual problems are exposed. Larry et al dupe people by effect slogans, that give the false impression of certainty of evolution. And when the truth is uncovered, the standard answer is: "We are working on it". Or: "We don't know yet". As if evolution would be the answer in the future, no matter what. Aren't these not a prima facie of " evolution of the gaps" arguments ? The question is: If a certain line of reasoning is not persuasive or convincing, or only leads to dead ends, then why do proponents of materialism not change their mind because of it? The more scientific papers are published, the less likely the scenario of large scale evolution without intelligence becomes. The gaps are NOT being closed. They widen more and more. Some evolutionary predictions have even been falsified. We should consider the fact that modern biology may have reached its limits on several key issues and subjects. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios, or in a confession of ignorance. Fact is there remains a huge gulf in our understanding… This lack of understanding is not just ignorance about some secondary details; it is a big conceptual gap.

      The reach of the end of the road is evident in the matter of almost all major questions. The major questions of evolutionary novelties are very far from being clearly formulated, even understood, and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, evolution is a fact. We don't know yet, therefore evolution and abiogenesis ? That way, the design hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence does not provide satisfactory explanations through naturalism, why should we not change your minds and look somewhere else ? I see only one reason : there is a emotional commitment to naturalism. Reason is not on the side of the materialist. The believer in creation IMHO has good reasons to hold his world view. Reason is on his side. The evidence points massive in that direction. Of course Larry et al are now ready with the answer on their tongue: " Argument from ignorance", they scream. Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. ( Contrast this with Popperian falsification, where propositions are corroborated to the degree that they successfully withstand attempts to falsify them ) Provided the proposition, together with its competitors, form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. As Sherlock Holmes famous dictum says : when you have eliminated the impossible, whatever remains, however improable, must be the truth.

      Delete
    18. Hi, Ontangello.

      Can you give a precise account of how I got to work this morning, down to the last millimeter of every single step I took?

      If you cannot, would you have to accept my claim that I was magically transported there thru supernatural means?

      Delete
    19. "Instead of compelling answers, questionmarks and lack of understanding, generalized ignorance, and conceptual problems are exposed."

      The quintessential argument from ignorance on display. Watch how Otangelo now copy-pastes his pre-made response that claims he's not making an argument from ignorance, despite it being manifestly what he's doing.

      Delete
    20. Stop whining, Mikkel. Its pathetic.

      Delete
    21. "Fact is there remains a huge gulf in our understanding… This lack of understanding is not just ignorance about some secondary details; it is a big conceptual gap."

      And that's all you have to go on, Otangelo, arguments from ignorance. You haven't one whiff of evidence in favor of your 'intelligent design' scam.

      You haven't even shown that it is impossible for irreducible complexity to evolve by naturalistic means. You only point out incomplete knowledge of purely naturalistic systems, or you beg the question by defining IC systems as impossible to evolve. Tautologies are not evidence.

      Delete
  6. "It's pretty frustrating. I probably shouldn't respond to kooks, especially those who think they are experts in biochemistry" [SNIP}

    Writing as someone who comes to this site to learn, why do you persist in doing it?

    "I learned long ago, never to wrestle with a pig. You get dirty, and besides, the pig likes it."

    ReplyDelete
    Replies
    1. I keep hoping that others might learn by reading my responses. At the very least, I hope to expose the stupidity of the IDiots and their dishonesty.

      Delete
    2. So far, you utterly fail, Larry......

      All you are doing, is exposing the bankrupcy of your world view, and naturalistic explanations, which are nothing more then wishy washy wishful superficial just so stories for the uneducated average people which blindly trust people like you.

      Delete
    3. Pathetic, OG. "[U]neducated average people," who write articles with titles like this:

      Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy

      That's from the American Journal of Human Genetics, March 31, 2016. I get monthly newsletters informing me of articles in this peer-reviewed academic journal and others, and I'm not even a scientist, just an interested layperson.

      Tell me which part of the research in the article I named (or any other article in this journal) consists of "superficial just so stories." It didn't seem superficial at all to me, or a "just so story."

      It is just this sort of technical research (huge amounts of it every year from all over the world) that supports and is supported by the biochemistry that Larry has literally written the textbook about, and for the evolutionary biology that is inextricably intertwined with it.

      And if I do not acknowledge anything, it is indeed because i rarely fail.

      Trying out a second career in comedy?

      Delete
    4. judmarc

      the fairy tale story that Larry, PZMyers, Jerry Coyne, Richard Dawkins, Bill Nye, and all proponents of evolution believe and adhere to, has literally EXPLODED. Evolutionary novelties through mutations, migration, genetic drift, and natural selection is a prediction that HAS BEEN FALSIFIED through the good work of dedicated scientists, that are exposing the REAL mechanisms that produce organismal form and shape. Science has uncovered that membrane targets and patterns, cytoskeletal arrays, centrosomes, ion channels, and sugar molecules on the exterior of cells (the sugar code), and Gene regulatory networks are the determinant factors of cell shape and organisation of multicellularity. In short the whole cell and epigenetic mechanisms are involved. Change does not happen solely on the genetic level. The sole reason that Darwins theory has not been given up by a major number of scientists is due to their philosophical background; once that evolution has been engrained in their minds, its hard to remove it. And that is the case, because generations of scientists have been brainwashed with philosophical and methodological naturalism, where intelligent causes are excluded a priori. But things are changing. I predict that within our generation, things will be different. The truth cannot be remained hidden for much longer. Larry et als views will be history of a distant past.

      Delete
    5. In short the whole cell and epigenetic mechanisms are involved.

      Please post citations to peer reviewed journal articles on how long the effects of these epigenetic mechanisms last.

      If you keep an open mind, maybe you'll learn something from these citations.

      Delete
    6. Otangelo,

      Your entire argument seems to be based on the premise that "irreducibly complex" entities cannot be the result of evolutionary processes. To my knowledge, no proponent of creationism has ever actually demonstrated why this must be the case. Yourself included. If I am mistaken about that, please present the evidence here.

      TIA.

      Delete
    7. "he fairy tale story that Larry, PZMyers, Jerry Coyne, Richard Dawkins, Bill Nye, and all proponents of evolution believe and adhere to, has literally EXPLODED."

      Among other things you don't understand (evolution, philosophy, science and even thought), is the word 'literally'.

      Delete
    8. "And that is the case, because generations of scientists have been brainwashed with philosophical and methodological naturalism, where intelligent causes are excluded a priori. But things are changing. I predict that within our generation, things will be different. The truth cannot be remained hidden for much longer. Larry et als views will be history of a distant past."

      That statement is nothing short of delusional. You are so thoroughly misinformed it isn't even funny. To think that religious propaganda has so totally disconnected your views from reality is depressing.

      Delete
    9. lutesuite

      thats a good start :

      Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning
      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413735/

      Principles of planar polarity in animal development
      http://dev.biologists.org/content/138/10/1877

      Morphogenetic Systems as cognitive agents
      http://ase.tufts.edu/biology/labs/levin/research/newdirections.htm

      Research on the Dynamics of Information Processing in Biological Structures
      http://ase.tufts.edu/biology/labs/levin/research/index.htm

      Molecular pathways regulating mitotic spindle orientation in animal cells
      http://dev.biologists.org/content/140/9/1843

      Evolutionary bioscience as regulatory systems biology
      http://www.sciencedirect.com/science/article/pii/S0012160611000911?np=y

      Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution
      http://bejerano.stanford.edu/readings/public/80_Function_GCRs.pdf

      the various epigenetic codes in the cell:

      CONTROL OF TRANSCRIPTION BY SEQUENCESPECIFIC DNA-BINDING PROTEINS
      http://www.garlandscience.com/res/pdf/9780815341291_ch08.pdf

      The transcription factor code: defining the role of a developmental transcription factor in the adult brain.
      For the human brain to develop and function correctly, each of its 100 billion neurons must follow a specific and pre-programmed code of gene expression. This code is driven by key transcription factors that regulate the expression of numerous proteins, moulding the neurons identity to create its unique shape and electrical behaviour.
      https://www.findaphd.com/search/projectdetails.aspx?PJID=41943

      Unraveling a novel transcription factor code determining the human arterial-specific endothelial cell signature
      Our pioneering profiling study on freshly isolated ECs unveiled a combinatorial transcriptional code that induced an arterial fingerprint more proficiently than the current gold standard, HEY2, and this codeconveyed an in vivo arterial-like behavior upon venous ECs.
      http://www.bloodjournal.org/content/122/24/3982?sso-checked=true

      The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding.
      The term 'transcriptional regulatory code' has been used to describe the interplay of these events in the complex control of transcription. With the maturation of methods for detecting in vivo protein-DNA interactions on a genome-wide scale, detailed maps of chromatin features and transcription factor localization over entire genomes of eukaryotic cells are enriching our understanding of the properties and nature of this transcriptional regulatory code.
      http://www.ncbi.nlm.nih.gov/pubmed/16647254

      The Splicing code
      rigin and evolution of spliceosomal introns
      http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-7-11

      The rna binding protein binding code
      A compendium of RNA-binding motifs for decoding gene regulation
      http://www.nature.com/nature/journal/v499/n7457/full/nature12311.html

      microRNA binding code
      The code within the code: microRNAs target coding regions
      http://www.ncbi.nlm.nih.gov/pubmed/20372064

      The Glycan or Sugar Code
      Biological information transfer beyond the genetic code: the sugar code
      http://www.ncbi.nlm.nih.gov/pubmed/10798195

      Delete
    10. Nasrudin was caught in the act and sentenced to die. Hauled up before the king, he was asked by the Royal Presence: "Is there any reason at all why I shouldn't have your head off right now?" To which he replied: "Oh, King, live forever! Know that I, the mullah Nasrudin, am the greatest teacher in your kingdom, and it would surely be a waste to kill such a great teacher. So skilled am I that I could even teach your favorite horse to sing, given a year to work on it." The king was amused, and said: "Very well then, you move into the stable immediately, and if the horse isn't singing a year from now, we'll think of something interesting to do with you."
      As he was returning to his cell to pick up his spare rags, his cellmate remonstrated with him: "Now that was really stupid. You know you can't teach that horse to sing, no matter how long you try." Nasrudin's response: "Not at all. I have a year now that I didn't have before. And a lot of things can happen in a year. The king might die. The horse might die. I might die.

      "And, who knows? Maybe the horse will sing."

      Delete
    11. You don't seem to have understood my question, Otangelo, because nothing on that list of things to copy/pasted remotely addresses it. Here's my question again. If you need it explained for you further, I can try:

      Your entire argument seems to be based on the premise that "irreducibly complex" entities cannot be the result of evolutionary processes. To my knowledge, no proponent of creationism has ever actually demonstrated why this must be the case. Yourself included. If I am mistaken about that, please present the evidence here.


      Delete
    12. lutesuite

      Well, maybe to add to your knowledge....

      Fe-S clusters play a key role in the electron transport of photosynthesis, and are thought to belong to the oldest structures existing in biological cells. FeS cluster biogenesis is an essential process basically in all life forms. The capacity of the Fe atom in Fe-S clusters to take up an electron provides the required electron carrier capacity in these pathways. FeS cluster assembly is a complex process requiring the uptake of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to special assembly sites in the cell, and their insertion into apoproteins. Iron-sulfur assembly proteins are required for the biological formation of these clusters. These ancient and essential components of the cell machinery depend on iron and sulfur. There is however a special problem. Free iron and sulfide released by FeS clusters are toxic to cells; complex mechanisms are therefore needed to coordinate the synthesis of these clusters, and these pathways have to be compartmentalized in the respective organelles. Nar1 is a essential component of the Fe/S protein assembly machinery. Required for maturation of Fe/S proteins. Nar1 itself however is both a target and a component of the cellular Fe/S protein biogenesis machinery creating an interesting “chicken and egg” situation for its maturation process, since Nar1 itself contains two Fe/S prosthetic groups.

      Iron–Sulfur (Fe–S) clusters are also needed in the active site of enzymes and proteins, required for DNA replication and repair. Therefor, they had to exist prior life began. These DNA replication enzymes imho also require complex proteins and enzymes for their biosynthesis. Thats also a classical chicken/egg problem.

      A further issue is that when life began, there had to exist assimilatory ferric reductases which were essential components of the iron assimilatory pathway that generate the more soluble ferrous iron, which is then incorporated into cellular proteins. In plants, these enzymes reduce Fe(III) to Fe(II) which is more soluble and can be taken up by the IRT transporters at the root surface of plants.


      A few things to think about : How did the FE/S assembly machinery arise ? It could have not happened through evolution, since dna replication and repair depends on proteins that use FE/S clusters. How did the machinery arise to protect the cell from FE/S clusters, toxic to cell, and so the coordination of the synthesis process ? Had the coordination and protection not have to exist from day one, and so the compartmentalization, since without that, the cell would die ? What came first, Nar1 component, using two FE/S clusters, required to synthesize FE/S clusters, or FE/S clusters ? How did the compartmentalization take place ? Had it not have to be right from the beginning of the life of the cell, otherwise the cell would die ?

      Delete
    13. "Naked" ion-sulfur clusters are catalysts, they catalyze the same chemical reactions the enzymes that use them do, just much less efficiently and much less specificly. Nevertheless, they still work.

      That's it, that's your entire argument rendered irrelevant. What next?

      Delete
    14. Mikkel

      next is that FE/S clusters generate harmful hydroxyl radicals and are therefore harmful for RNA molecules.... So you have still some work to do to refute my argument.

      Delete
    15. "next is that FE/S clusters generate harmful hydroxyl radicals and are therefore harmful for RNA molecules.... So you have still some work to do to refute my argument."

      [Citation needed]

      Delete
    16. Still no answer to my question, Otangelo, despite all that copy/pasting. Do you not understand the question? Do you need it translated into another language? Or is it just you're afraid to admit you can't answer the question? That's nothing to be ashamed of. The most brilliant minds (cough) of the Intelligent Design Creationist movement, whether Behe, or Dembski, or Luskin,or O'Leary, have all failed to answer it as well.

      Delete
    17. lutesuite

      or is it maybe that for you, any evidence " is not good enough " not matter what to infer ID as the best explanation for the matter in question , simply, because you don't wan't to ? Where you start will often determine where you will end. If you search for a Intelligent Designer only to show yourself that He is not there, then you will not find Him. There are just personal preferences of explanations and world views for all that exists. So rather than say, there is no natural phenomena and scientific evidence, that is best explained through design, you should say : Intelligent design is not my peferred explanation, for whatever reasons.

      Do you have actually reasons to reject the design inference, and prefere the naturalistic explanation for the issue in question ?

      Delete
    18. More diversionary tactics. Just answer the question, Otangelo, or admit that you can't and join the rest of your creationist brethren in the "fail" line.

      Delete
    19. I do, however, appreciate your honesty in admitting that your belief in the "design inference" is just a matter of wishful thinking on your part, and not a conclusion based on an objective assessment of the scientific evidence. So due credit to you for that.

      Delete
  7. Heh, I had an argument with Otangelo about photosynthesis too. He claimed that chlorophyll biosynthesis couldn't possibly evolve because the last steps in the pathways, he claimed, requires 16 "unique enzymes not found anywhere else in life".

    2 minutes on google showed every enzyme in the pathway belongs to well-characterized protein superfamilies with homologoues for all of them, significantly predating chlorophyll biosynthesis.

    He then switched the claim to saying there'd be no reason to evolve any of these enzymes, because only the last step in the pathway (the final step resulting in chlorophyll) results in a functional and useful molecule. Anoter 2 minutes on google showed every step in the pathway results in an intensely photoactive molecule.

    He also claimed that the photosystem could not possibly evolve from the cytochrome complex because it would have to somehow magically find it's way into and become embedded in the membrane, which requires special membrane-compatible 3D structures that would have to evolve gradually, but couldn't because it wouldn't be functional before the end-system. The cytochrome complex is already a membrane-embedded system.

    The rule of thumb with Otangelo is: Everything he says is diametrically opposite to demonstrable fact.

    ReplyDelete

  8. Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eigth last steps are used by specific enzymes uniquely in this pathway. The pathway must go all the way through, otherwise chlorophyill is not synthesized. Therefore, the Chlorophyill biosynthesis pathway is irreducible complex.

    ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

    Your answer ?

    This organism randomly evolves new enzymes here and there by standard means (duplication and sub/neo-functionalization as has been directly observed happening many time and we can prove happened in the past using Ancestral Sequence Reconstruction). Some of these enzymes modify Porphyrins (the precursors of Heme and Chlorophyll) such that they alter it's properties in useful ways. This happens multiple times, in useful ways making them retained by natural selection, giving additional steps to the pathway to Chlorophyll.

    The problem however is not solved with this answer.

    What good would there be, if the pathway would go only up to the 15th step ? none
    What good would there be, if the pathway would go all the way through the 17th step ? Chlorophyll would be produced , BUT :
    What good would there be for chlorophyll by its own, if not fully embedded in the photosyntesis process ? none.
    What good would there be for a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?
    What good would there be for photosynthesis without chlorophyill in place, capturing light, and transmitting it to the photosystem ? none, since capturing light is essential for the whole process.

    There is another major problem:

    Chlorophyll itself, and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis.

    Furthermore, chlorophylls are embedded in the light harvesting complex. But to be so, binding proteins must be in place, which during assembly bind chlorophyll to it.

    Question : Why would natural processes evolve binding proteins, if there were only use for them, once pigment molecules and the light harvesting complex existed? If chlorophyll evolved before the antenna proteins that bind it, it would in all likelihood destroy the cell, so the proteins had to evolve first. But natural selection could not favour a ‘newly evolved’ protein which could bind chlorophyll and other pigment molecules before those crucial pigments had themselves come into existence! Each binding site must be engineered to bind chlorophyll a or chlorophyll b only or carotene only. The carotene molecules must be present in just the right places for quenching triplet states in the chlorophylls. Even if the pigment molecules were already around, producing just the right protein would be an extremely difficult task. It would not only have to bind pigment molecules only, but it would need to bind just the right pigments in just the right places in just the right orientation so that energy could be transferred perfectly between them, with a little lower energy at each step. Anything else would do nothing, or would transfer energy at random, and the complex would accomplish nothing at best and burn up the cell at worst.

    ReplyDelete
    Replies
    1. "The problem however is not solved with this answer.

      What good would there be, if the pathway would go only up to the 15th step ? none"


      But that's false you idiot, which is the entire point. The molecule at the 15th step is still functional, just slightly different. It just responds to slightly different wavelengths of light.

      "What good would there be for chlorophyll by its own, if not fully embedded in the photosyntesis process ? none."

      It was never not part of the process of photosynthesis, for fucks sake. The entire structure is homologous to the cytochrome BC complex, that's the point. With alterations to the cytochrome complex, it becomes a photosensitive complex instead. Long before chlorophyll biosynthesis had evolved. The previous steps in the pathways are all still photoreactive molecules. I quoted entire book sections on biochemistry at you that demonstrate this before. Why are you still ignorant of facts that have been presented to you?

      "Question : Why would natural processes evolve binding proteins, if there were only use for them, once pigment molecules and the light harvesting complex existed?"

      Because they weren't useless before the whole modern light harvesing complex existed, they are derivations of molecules that act on heme and related compounds.

      All your assumptions are wrong. You are making claims about whether previous steps in some pathways would function or be useless without having bothered to check. You are in effect just making shit up as you go along. Lying for Jesus.

      Delete
    2. @Larry Moran: "Moving the goalposts?"

      He never acknowledges refutation. Once something has been refuted, he just proceeds on to something else as if history just started over.
      Either he completely ignores the refutation and moves on to something else, or he just brainlessly denies the refutation and frequently quotes the same shit all over again as if the mere assertion of it is thereby unassailable.

      He seems to operate under the principle that "If I, Otangelo Grasso, says something, it is thereby true and cannot be refuted no matter what and I never need to check anything".

      Delete
    3. But that's false you idiot//

      Education was never your strenght, isn't it, Rumraket?

      The molecule at the 15th step is still functional

      Evidence, please ?

      The entire structure is homologous to the cytochrome BC complex

      What ??!! Would you mind to explain, please ??!!

      With alterations to the cytochrome complex, it becomes a photosensitive complex instead

      kkkk...... really ?? no kidding.....

      From the book you quoted:

      The useful step in this biosynthetic chain was only reached when uroporphyrinogen and its oxydation products were formed.

      That is in the 6th step of the pathway. So my point remains valid. There is no useful intermediate between the first and sixth step, so why would natural mechanisms come up with these enzymes and intermediate products ??!!

      The porphobilinogen synthase in the fourth step is particulary interesting: Once a hexamer is formed, hydrolysis allows hydroxymethylbilane to be released, as well as cofactor regeneration


      The reaction catalysed by PBGD involves the formation of preuroporphyrinogen, a linear tetrapyrrole (bilane), by the extension of an enzyme-bound DPM (dipyrromethane) cofactor that acts as a reaction primer 4)

      Question: how could evolution have produced this complex function ? It had to program into the genome the specification for the production of the co-factor molecule, and its function of extension binding of intermediates during the catalytic reaction at the right place, at the right moment, in the right sequence.

      Furthermore:
      how did gene duplication, followed by random mutations and natural selection figure out to produze the PBG deaminase enzyme,, used as far as reported, exclusively in this path way, so no co-option possible ? - that would produce this complex reaction, ( which is just the third in the whole heme and chlorophyll biosynthesis pathway of total 8 and 17 steps ) consisting in 4 highly coordenated , ordered, sequenced and complex steps, forming a geometrically correct tetrapyrrole, and repeat the first two steps in total 4 times ? and furthermore use co-enzyme molecules ? Could evolution be a feasable mechanism ? How did evolution be capable to produce the right genetic code and informational sequence ? The genetic code uses average over 300 thousand nucleotides in the sequence. How did evolution figure out to program the release at the end of the process of the hydroxymethylbilane enzyme from the reaction at the right time, after the linear hydroxymethylbilane product is catalized, and while releasing four ammonia molecules ?

      Because they weren't useless before the whole modern light harvesing complex existed, they are derivations of molecules that act on heme and related compounds.

      Heme does not require 17 biosinthetic steps to be produced...

      Delete
    4. Larry

      i am answering precisely to each point Rumraket raised.

      Where is your answer to my post above, where i addressed your questions ?

      Delete
    5. Rumraket: He never acknowledges refutation.

      Haha. Show me ONE post of yours, where you acknowledged what i said. Just one.....kkkkk

      And if I do not acknowledge anything, it is indeed because i rarely fail. In the OP Larry quoted actually is a evident mistake, which nobody here pointed out......

      Delete
    6. "The useful step in this biosynthetic chain was only reached when uroporphyrinogen and its oxydation products were formed.

      That is in the 6th step of the pathway. So my point remains valid. There is no useful intermediate between the first and sixth step, so why would natural mechanisms come up with these enzymes and intermediate products ??!!"


      Useful for photochemistry, uroporphyrinogen is still a heme precursor. For fucks sake. Just as with the chlorophyll precursors after the branch-off to heme biosynthesis, there's no reason to think these precursors were always entirely nonfunctional just because only the end-product is being used today in extant organisms. It's the same fucking concept all over again.

      Will you ever allow yourself to think?

      Delete
    7. "how did gene duplication, followed by random mutations and natural selection figure out to produze the PBG deaminase enzyme,, used as far as reported, exclusively in this path way, so no co-option possible ?"

      Look for homologous proteins.

      Delete
    8. Thanks for the last two responses, Mikkel, helping to clarify that among his many sins, O. Grasso includes the old tiresome unevidenced (actually counterfactual) prohibition of genetic drift.

      Delete
    9. "Haha. Show me ONE post of yours, where you acknowledged what i said. "

      What a strange request. What do you mean by "acknowledge what you say"? You say what you say I hereby acknowledge. So what?

      Every post of mine is a direct response to yours, including this one. This isn't about acknowledging the mere existence of your posts, it's about you acknowledging and understanding when our posts contain functionally valid rebuttals and refutations of the contents of yours, both at a specific case-by-case basis and an overall conceptual level.

      We have shown that both the concept of irreducible complexity is irrelevant to evolution (that would be a refutation at a conceptual level), AND we have shown that some of the structures you think are IC, actually aren't (which would be a refutation of a specific case).

      I cannot express myself any more clearly than this. How come, after all this time, you still do not understand why irreducible complexity is not an obstacle to evolution? Why can you not fathom this?

      Delete
    10. there's no reason to think these precursors were always entirely nonfunctional just because only the end-product is being used today in extant organisms.

      haha. There is no reason to believe there are no flying cups surrounding neptun....

      Delete
    11. "There is no reason to believe there are no flying cups surrounding neptun"

      But that's trivially false. Cups are human inventions and there'd be no reason to send them into orbit about Neptune. So there is in fact reason to believe there are no flying cups surrounding neptune.

      Try again kiddo.

      Delete
    12. Otangelo-
      You are wrong to say something couldn’t evolve.
      Anything can evolve from nothing.
      It would be more accurate to say that the current theory of evolution (and modern physics) allows for the human being to spontaneously assemble from dust than it is to say that something could not evolve using natural processes.

      There is no “IC’ that could falsify the current theory just as there is no observation of any kind that would falsify the theory- anything can happen at random.

      There is no observation that can falsify ‘intelligent design’ either, as we have no metric of design or intelligence.

      You ask which makes for the better explanation- a reasonable question given that neither explanation can be falsified.
      When you present your information it would be much better if you would acknowledge that whatever system you are looking at could have evolved given that anything can happen.
      Of course whatever system you are looking at could be the result of intelligent design as well.

      Your question of ‘best inference’ then can be based on the actual evidence instead of false claims about the subjects under discussion. And of course we should acknowledge that ‘best inference’ and ‘personal incredulity’ are about the same thing when it comes to metaphysical type inferences.

      Delete
    13. Jack Jackson: we have no metric of design or intelligence.

      Of course we do. You seem not to be well informed.

      In order to make design prediction, it must be established what can be recognized as design in nature :

      Something having the PROPERTIES that we might attribute to that of a designed system:
      1) IRREDUCIBLY COMPLEX
      2) Acts as an informational processing systems, -
      3) a system which uses some form of digital code, translated into instructions by another universal language translation (universal genetic code). This is LANGUAGE, MEANING.
      4) Appearance of highly complex dependencies thus giving the appearence of Implicit intelligence (although not intelligent itself, indicates an origin involving intelligence.. )
      5) use of molecular machinery on a scale and complexity which mankind has never IMAGINED possible - all with appearence of exact purpose, intent, function and dependencies
      6) exhibiting logical functional layers - regulatory genes controlling gene expression - conceptually teh same as a logical software layer controlling teh underlying system.
      7) another layer of complex 3 Dimensional control and access, and adaptation to environment: Epiogentics.
      8 Implicit built in ERROR checking from the get go: reducing mutations to a minimal
      9) Display the DESIGN of complex software, designed to adapt and EVOLVE in a very controlled and careful way - while at the same time minimizing mutations. A system designed to EVOLVE and SURVIVE. (gene splicing ) ..
      10) Something which as well as exhibiting all of the above, also has no conceptual way of coming into existence through naturalistic means, : or something whose existence and origins appears to defy all known scientific understanding. Something which requires the application of alot of FAITH and IMAGINATION of some theories to describe its origins through natural means alone.
      So the application of COMMON SENSE and inference, from observations from the world around us (information processing systems) might indicate to us certain things having these above PROPERTIES, would fall into the category of things that have been DESIGNED.
      One of the most intelligent concepts in the known universe is the concept of Evolution itself.

      Delete
    14. Ontnagelo Rosso,

      I've learned one but very important thing over the year that I hope you did as well, but you've just have forgotten about it....

      You absolutely CAN'T convince people to believe in the very simple facts and truths IF THEY DON'T WANT TO, OR EVEN WORSE, REFUSE TO ACCEPT THE TRUTH. What are you going to do about it if it is true???

      Delete
    15. "there's no reason to think these precursors were always entirely nonfunctional just because only the end-product is being used today in extant organisms.

      haha. There is no reason to believe there are no flying cups surrounding neptun...."

      Absent any evidence you can produce to prove that the precursors were always non-functional, your claim of IC is as worth considering as flying cups around Neptune.

      Delete
    16. Otangelo-
      Of course you can come up with reasons to think something was designed- and you can attribute that design to intelligence if you want to.

      But we have two distinct problems-
      1- not all things designed exhibit any or all of the PROPERTIES you list.

      2- Not all things with the PROPERTIES you mention are the result of intelligent design.

      From those two problems we can see how one could use your list strictly on the basis of personal incredulity. And that was my point.

      You failed to acknowledge current theory can allow for anything to happen.

      Delete
    17. Eric says,

      "What are you going to do about it if it is true???"

      Who is "you" and what is "it" that you claim is true? Is this some weird form of Pascal's Wager?

      Delete
    18. Eric says,

      "You absolutely CAN'T convince people to believe in the very simple facts and truths IF THEY DON'T WANT TO, OR EVEN WORSE, REFUSE TO ACCEPT THE TRUTH."

      Your pathological projection aside, more worrisome is your smug assumption your know the "truth" about any of this, without any convincing evidence to present.

      Delete
    19. OG keeps asking, "Why would enzymes evolve" some particular trait, when he should be asking, "How could enzymes evolve" that trait. The distinction seems small, but I think it's critical.

      When OG asks "Why" he assumes that the process involves a kind forethought, planning, design. This is begging the question.

      OG doesn't find a satisfying answer to the question, "Why" in an answer to the "How" question, and much talking past one another ensues. Of course, this isn't his only logical problem, but it's a basic one.

      Delete
    20. bwilson295-
      If you turn it around you can see the entire problem--
      Answering a 'why' question with a 'how' answer is a logical fallacy.

      Now you understand why the people asking 'why' questions consider the enterprise of coming up with 'how' answers to be basically fallacious- because every answer you give is not an answer to the actual question the person has.

      Have you noticed that no level of detail of 'how' is ever good enough?
      That's because 'how' never answers 'why'.

      The creationist begs the question and wants to know 'why'.
      Coming back with long descriptions of 'how' isn't really a logical activity, although I appreciate the details of some of the processes.


      Delete
    21. The creationist assumes that there's a "why" answer that he would find satisfying. (He begs the question.) In evolution, the only real answer to "why" is "because it could," or a whole lot of detailed "how" answers involving the timing of specific mutations, population sizes, effects of the mutation on the probability of reproduction in particular environments, and luck (randomness). These are not satisfying if you want a deep "Why" answers, but sometimes asking the deep "Why" question is inappropriate.

      For example, people ask "Why did this tree fall with no warning as I walked past, paralyzing me?" or "Why was my child born with this serious birth defect?" The answers may well be "because the tree was slowly rotting and the soil was soft from the rain, and it fell, and you happened to be there because you got up early and walked to the store to buy milk" or "because somewhere among the ancestors of both you and your spouse, mutations occurred in the relevant gene, and in series of 1/2 chances per generation for each of you, you both inherited it, and therefore there was a 1/4 chance this child would have two copies of it and be harmed, and he was." Are these causes emotionally satisfying? No.

      We want the explanation to be more goal-directed, more personal. We want an answer to the "why" question, but asking "why" questions when the only answers there can be are "how" answers, isn't really a logical activity.

      Delete
    22. " You failed to acknowledge current theory can allow for anything to happen. "

      Putting blind faith into evolution much ?? There is a basic problem: if you change the size of a piston, you need to change the size of the motor block that hosts the cylinder, and a series of other parts not directly matching with the piston. So if you change one thing in a motor, many other parts have to change as well. If there is a mutation in a gene that expresses one protein, would there not have to be a simultaneous mutation in another nearby gene that expresses the counterpart that matches with the first protein, in order for both to match again together ? If you change the key, does the lock not have to change together ? How could that be different in biological systems ?

      Soren Lovtrup, professional biologist in Sweden, said


      "...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."


      Delete
    23. ""...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."

      The whole problem with your argument. You don't know (and neither did Soren Lovtrup) that incipient and intermediate stages are not advantageous. "Intermediate" may allow you to obfuscate your way out of providing evidence, but "incipient" does not.

      Produce empirical evidence that incipient stages of any 'irreducibly complex' system were not advantageous.

      Delete
  9. If you want to have fun with Angelo, ask him to provide a summary of which statements are his own from the plagiarized material he's used in his OP's and replies.

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    1. That would be interesting. Perhaps Angelo posts under 20 different names at dozens of other sites.

      Delete
    2. If he says something coherent, it's usually not himself that wrote it.

      Delete
    3. If he says something coherent, it's usually not himself that wrote it.

      Has he ever said anything coherent?

      Delete
  10. @ Rumraket

    You ever feel like you woke up in the middle of the movie Ground Hog Day?

    ReplyDelete
  11. A long time ago I had heard of a process by which IC biochemical pathways can evolve by what is known as 'retrograde evolution'. For brevity, lets start a little after the beginning (and the beginning is easily explained, btw). So lets start where molecule F is converted to molecule G by an enzyme. So:
    a) F-->G
    There is now selection pressure for more molecule F, b/c its supply is limited, and so any lineage that can come up with new or better ways to make F are more fit. A solution is found by gene duplication or by other means, and...
    b) E-->F-->G.
    Now there is selection pressure to come up with more E, because that is in short supply, and eventually another enzyme is co-opted, and...
    c) D-->E-->F-->G
    By now you know the drill:
    d) C-->D-->E-->F-->G
    e) B-->C-->D-->E-->F-->G
    f) A-->B-->C-->D-->E-->F-->G

    So in this pathway the most primitive step made G, and the most recently evolved step was to make A. Here is what would become an IC pathway since no modern cell can make G except thru F, and they cannot make F except thru E, and so on. But its origins were anything but supernatural.

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    1. That insight was by Norman Horowitz in a paper in PNAS in 1945.

      Delete
  12. Thanks! And in less than a minute I found a lot of info about that, plus a related means of pathway evolution called patchwork evolution. Both of these seem pretty satisfying. I am no biochemist or professional evolutionary biologist, but even I know that many metabolic pathways have adjacent steps carried out by homologous enzymes (like would be predicted from retrograde ev.) and different pathways have similar steps carried by homologous enzymes (as would be the result of patchwork ev.).

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  13. Dear Dr. Moran, thanks for all the effort. I teach Evolution in Mexico and I think it is very useful to show to the students how ID people have a hidden agenda and systematically avoid critical thinking.

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    1. I second rems' sentiment!

      I found this thread very illuminating.

      In broad strokes – to summarize in terms simple enough for

      1 - a high school Biology teacher to explain in class and

      2 - see if I can even push the envelope further.

      Light-driven proton pumps emerged as an evolutionary afterthought (as it were) to do the job of alkaline vents as described in Nick Lane’s book describing the chemo-osmotic origins of life.

      These light sensitive proteins were then co-opted to evolve sensory receptors important in bacterial phototaxis. These same proteins were then subsequently co-opted in the convergent evolution of eyes.

      Essentially, we are all seeing with bacterial eyes.

      I seem to remember a paper in the popular press with that catchy title somewhere, but for the life of me cannot find it. I would be grateful if anybody could refer me to it.

      Delete
    2. On the topic of irreducible complexity (and for the benefit of my high school students) - I want to see if I can summarize Larry's synopsis


      Nobody believes that photosynthetic bacteria are that ancient. The "blue green algae" are cynaobacteria.

      Their dual photosystems clearly evolved late from a combination of a type I reaction center in species like Heliobacter and green sulfur bacteria and a type II reaction center from species like purple bacteria and green filamentous bacteria.

      The oxygen evolving complex was a late addition.


      The steps of photosynthesis can be broken down into events occurring in the electron transport chain of the inner membrane (which emerged earlier in evolution) and Calvin cycle events occurring in the stroma (which emerged later in evolution).

      The events occurring in the inner membrane are NOT “irreducibly complex” and can be basically broken down into two complementary events:

      1 - events leading to the generation of useful ATP (photosystem II) and

      2 - events leading to the generation of useful NADP (photosystem I)

      Continuing on the subject of Complex Irreducibility, both photosystems employ Porphyrins and Carotenoids which are important in various metabolic processes(not just photosynthesis) meaning their evolutionary history may reflect many other functions only to be co-opted later for photosynthesis. Meanwhile both can be demonstrated to have abiogenic origins.

      On the subject – I just want to share part of an essay question from the 2013 AP Biology exam:

      Bacteriorhodopsin has been found in aquatic organisms whose ancestors existed before the ancestors of plants evolved in the same environment. Propose a possible evolutionary history of plants [based on previous information already provided in the stem of the question] that could have resulted in a predominant photosynthetic system that uses only some of the colors of the visible light spectrum.


      I just posted that for general public interest and as a random act of mischief, by way of suggestion to some Creationists present, that they may benefit by attending a high school Biology class that adheres to the AP curriculum.

      Correction of or improvement to my scribbles above greatly appreciated and I thank any and all in advance.

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    3. Tom

      despite off topic, here some remarks:

      proton pumps are complex proteins. They could not have been produced prior life began through evolution, since evolution depends on DNA replication, and mutations through the replication process.

      Lane's claim:
      We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes.

      Sodium/proton (Na+/H+) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis 3
      NhaA is made up of two distinct domains: a core domain and a dimerization domain. In the NhaA crystal structure a cavity is located between the two domains, providing access to the ion-binding site from the inward-facing surface of the protein

      So there is actually nothing simple about this protein.

      Of course they could not be there, because they depend on all the complex cell machinery that makes proteins, which was obviously not there at this stage.

      At any stage before the dna-protein world, the presence of a non-random protein, no matter how simple, is forbidden.

      The problem with monomers is bad enough,but it is worse with polymers,e.g.,RNA and DNA,whose stability in the absence of efficient repair enzymes is too low to maintain genetic integrity. RNA and DNA are clearly too unstable to exist in a hot prebiotic environment. The existence of an RNA world with ribose appears to be incompatible with the idea of a hot origin of life.

      Furthermore:

      The argument follows, that perhaps life first originated in the ocean, then overtime evolved enough to come up to the surface to photosynthesize without getting burned by UVR. But even this theory has its own problems. Namely the problem of hydrolosis or “water-splitting.” The US National Academy of Sciences explains, “In water, the assembly of nucleosides from component sugars and nucleobases, the assembly of nucleotides from nucleosides and phosphate, and the assembly of oligonucleotides from nucleotides are all thermodynamically uphill in water. Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored at any plausible concentrations: polypeptide chains spontaneously hydrolyze in water, yielding their constituent amino acids,” (Luskin). Physicist Richard Morris concurs, “… water tends to break chains of amino acids. If any proteins had formed in the ocean 3.5 billion years ago, they would have quickly disintegrated,” (Morris, 167). Additionally, the cytoplasm of living cells contain essential minerals of potassium, zinc, manganese and phosphate ions. If cells manifested naturally, these minerals would need to be present nearby. But marine environments do not have widespread concentrations of these minerals (Switek). Thus, it is clear, life could not have formed in the ocean.

      And last not least:

      the electromagnetic radiation of the sun is restricted to a tiny region of the total electromagnetic spectrum, equivalent to one card in a deck of 10^25, and that the very same infinitely minute region is precisely that required for life. In addition both the atmospheric gases and water are opaque to all regions of the spectrum except this same tiny region. Denton concludes: "it is as if a card player had drawn precisely the same card on four occasions from a deck of 10^25"

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    4. At any stage before the dna-protein world, the presence of a non-random protein, no matter how simple, is forbidden.

      OG is fast becoming the king of the ludicrous statement. The building blocks of proteins (amino acids) have been found in meteorites, chunks of rock from the cold and vacuum of space. A few ordinary chemical bonds and voila, we have protein. Far from impossible, it's almost trivial: just stuff we know was sitting around in the early solar system plus ordinary chemistry.

      But perhaps we didn't need protein first. Many good scientists (sorry OG) have done excellent research (sorry again, OG) into the "RNA world" hypothesis.

      In any case, far from being stymied by impossibility, those looking into questions of the origin of life on Earth have several viable candidates to research.

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    5. Otangelo

      I am not convinced you are prepared to engage in an earnest exchange of ideas.

      In any case, any of my high school students could easily dismiss your thesis regarding the complex irreducibility of photosynthesis. As a matter of fact, I intend to use your original post in class to emphasize the importance of critical thinking as they sharpen their teeth by gnawing on your non sequiturs & ignoratio elenchi.

      ITMT, I urge you to read this excellent post by Larry Moran on evolution being more of a tinkerer than an engineer.
      http://sandwalk.blogspot.ca/2008/02/evolution-as-tinkering.html

      La sélection naturelle opère à la manière non d'un ingénieur, mais d'un bricoleur; un bricoleur qui ne sait pas encore ce qu'il va produire, mais récupère tout ce qui lui tombe sous la main.
      François Jacob, Le Jeu des possibles (1981)

      You have undertaken a conceptually impossible task.

      All the bits and pieces of photosynthesis were co-opted from pre-existing bits and pieces already available and already being employed elsewhere.

      For example, there exist various transitional versions of light-driven proton pumps exclusively involved in ATP synthesis and not photosynthesis per se.

      If you want to push your thesis of Complex Irreducibility, you will need to abandon your focus on photosynthesis (I surmise you have already conceded that point by your “moving of the goalposts”) and refocus on the complex irreducibility of metabolism which preceded photosynthesis (which you seem to be doing already).

      I also suggest you peruse Larry Moran’s “souper vs smoker” Metabolism First series of posts.

      In any case, I thank you for this opportunity to refocus my thoughts thereby permitting me to do a better job in my own class.

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    6. Tom Mueller

      Dembski wrote : The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability.Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other.

      So who has undertaken a conceptually impossible task ?

      All the bits and pieces of photosynthesis were co-opted from pre-existing bits and pieces already available and already being employed elsewhere.

      Thats one ot the typical just so assertions.

      ATP synthatse is a irreducible complex molecular motor par excelence. Disconnect one of its components, disturb one of its forms, replace some of your AA position, and the system loses function altogether. Try to build it slowly, step by step, by mindless unguided processes, where would the energy come from to build it, if it is the energy provider of life? Remember though that the energy that produces ATP synthase is essential to life, virtually for all forms of life. And unless the proton gradient is in place, ATPsynthase would be useless.

      Each of the below mentioned parts are ESSENTIAL and IRREDUCIBLE. Take away one , and ATP synthase ceases to function. Neither could any of the sub parts simply be co-opted from anywhere else. That would be the same as to say, in order to make a motor function, and a cylinder is missing, go search and find any cylinder nearby , co-opt it, and solved is the problem. The thing is that cylinders come in all size, specification, materials etc. And there is no goal oriented search of parts that fit through evolution Evolution has no forsight. Furthermore, there must be the information how and when and where to mount the parts, at the exact place, in the right sequence. Thats a far fetch for a mindless tinkerer to be able to achieve.

      1.The nucleotide binding stator subunits (“cylinders”) : The electrostatic interaction of these rotor and stator charges is essential for torque generation
      2.The central stalk (“crankshaft”) : The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. Is is essential.
      3, The A/V rotor subunit (“adapter”) ; It is not used in all ATP synthase motors, and can therefore be reduced.
      4. The Rotor ring (“turbine”) ; A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-
      ATPase.
      5.The Jon channel forming subunit ; Subunit a harbors the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface . The channel is essential for the operation of the enzyme, because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode
      6. The peripheral stalk (“pushrod”) ; The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit a in the membrane domain.
      7 - 11 do not exist in all atp synthase motors, and can therefore be reduced.

      Delete
    7. There are at least 5 subunit parts essential to mantain the basice function of the ATP synthase motor.

      ATP synthase is an irreducibly complex motor—a proton-driven motor divided into rotor and stator portions. Protons can flow freely through the CF0 complex without the CF1 complex, so that if it would have emerged first, a pH gradient could not have been established within the thylakoids. The δ and critical χ protein subunits of the CF1 complex are synthesized in the cytosol and imported into the chloroplast in everything from Chlorella to Eugenia in the plant kingdom. All of the parts must be shipped to the right location, and all must be the right size and shape, down to the very tiniest detail. Using a factory assembly line as an analogy, after all the otherwise useless and meaningless parts have been manufactured in different locations and shipped in to a central location, they are then assembled, and, if all goes as intended, they fit together perfectly to produce something useful. But the whole process has been carefully designed to function in that way. The whole complex must be manufactured and assembled in just one certain way, or nothing works at all. Since nothing works until everything works, there is no series of intermediates that natural selection could have followed gently up the back slope of mount impossible. The little proton-driven motor known as ATP synthase consists of eight different subunits, totalling more than 20 polypeptide* chains, and is an order of magnitude smaller than the bacterial flagellar motor, which is equally impossible for proponents of evolution to explain.

      A quick google search, and you will find the topic at my library. I am not linking it, otherwise my posts go into Larrys spam box.

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    8. Hi Otangelo

      Before continuing with an answer, I just want to confirm that you have abandoned the complex irreducibility of photosynthesis as untenable, that you have now shifted your target and you are now addressing the complex irreducibility of ATP Synthase.

      You acknowledge of course (as any high school student will confirm) that in evolutionary terms, ATP Synthase evolved before photosynthesis emerged (explaining, for example, why ATP Synthase is found in both mitochondria and chloroplasts)

      Delete
    9. A quick google search, and you will find the topic at my library. I am not linking it, otherwise my posts go into Larrys spam box.

      Here's the link. Otangelo Grasso has copied, word-for-word, from an article by Rick Swindell in the Journal of Creation volume 17 pages 74-84 (2003) [Shining light on the evolution of photosynthesis].

      Delete
    10. Otangelo says:

      "And last not least:

      the electromagnetic radiation of the sun is restricted to a tiny region of the total electromagnetic spectrum, equivalent to one card in a deck of 10^25, and that the very same infinitely minute region is precisely that required for life. In addition both the atmospheric gases and water are opaque to all regions of the spectrum except this same tiny region. Denton concludes: "it is as if a card player had drawn precisely the same card on four occasions from a deck of 10^25""

      I'd say it's least. It's certainly totally wrong. The Sun emits wavelengths over most of the electromagnetic spectrum, from radio to gamma rays. It emits very little gamma rays only because these tend to be absorbed by mass in the Sun and re-emitted in lower energy frequencies.

      If there is an intelligent designer, why did (s)he/it design and use chlorophyll for energy absorption? There are several forms of chlorophyll, each with somewhat different absorbance spectra, but they all absorb only a small fraction of the range of electromagnetic radiation emitted by the Sun.

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    11. Aham...

      Happily, our star (the sun) emits radiation (light) that is finely tuned to drive the chemical reactions necessary for life. But there is still a critical potential problem: getting that radiation from the sun to the place where the chemical reactions occur. Passing through the near vacuum of space is no problem. However, absorption of light by either Earth's atmosphere or by water where the necessary chemical reactions occur could render life on Earth impossible. It is remarkable that both the Earth's atmosphere and water have "optical windows" that allow visible light (just the radiation necessary for life) to pass through with very little absorption, whereas shorter wavelength (destructive ultraviolet radiation) and longer wavelength (infrared) radiation are both highly absorbed, as seen in Figure 3.{23} This allows solar energy in the form of light to reach the reacting chemicals in the universal solvent, which is water. The Encyclopedia Britannica{24} observes in this regard:

      Considering the importance of visible sunlight for all aspects of terrestrial life, one cannot help being awed by the dramatically narrow window in the atmospheric absorption...and in the absorption spectrum of water.
      It is remarkable that the optical properties of water and our atmosphere, the chemical bonding energies of the chemicals of life, and the radiation from the sun are all precisely harmonized to allow living systems to utilize the energy from the sun, without which life could not exist. It is quite analogous to your car, which can only run using gasoline as a fuel. Happily, but not accidentally, the service station has an ample supply of exactly the right fuel for your automobile. But someone had to drill for and produce the oil, someone had to refine it into liquid fuel (gasoline) that has been carefully optimized for your internal combustion engine, and others had to truck it to your service station. The production and transportation of the right energy from the sun for the metabolic motors of plants and animals is much more remarkable, and hardly accidental.

      http://www.leaderu.com/offices/bradley/docs/scievidence.html

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    13. "Aham..."
      Is that a biblical term?

      Anyway, happily or not, the Sun emits most of the electromagnetic spectrum, rendering the previous argument silly.

      And yet "intelligently designed" chlorophylls utilize so little of these finely tuned wavelengths. How does that bespeak of an intelligent designer?

      And the fact that life uses wavelengths which are available to it may be remarkable but is also necessary, or we would not be here to discuss it. You can claim a magical being made it all, but you have no evidence to back it up. Why did the intelligent designer allow things like sunburn and skin cancer if it is all so finely tuned? The fine tuning argument for ID is absurd. The vast majority of the volume of the universe is immediately lethal to life as we know it. Even large portions of the Earth are completely hostile to life. Recycling old, bad arguments is not helping your proof for an intelligent designer.

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    14. Happily, our star (the sun) emits radiation (light) that is finely tuned to drive the chemical reactions necessary for life.

      ...since without a Designer, the chemical reactions that occur on Earth (organic and inorganic) could just as well have been those suited for a totally non-Earthlike environment, right? :facepalm:

      To make it even simpler for you: Well duh, of *course* the chemical reactions that take place on Earth would be those that take place under the conditions occurring on Earth! This is like marveling that the coastline of the Mississippi looks exactly like the formations one would expect of rocks and soil carved by flowing water!

      By the way, is the Designer also responsible for the life that evolved without sunlight? Or is that the Devil? Just wanting to give credit where it's due....

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  15. Otangelo Grasso

    Before going to bed last night - I noticed you posed a question regarding the irreducible complexity of (OEC) involved in the photooxidation during photosynthesis.

    I seems to have vanished.

    ITMT - I want to be courteous and do the right thing by answering your earlier question on ATP Synthase.

    I just want to confirm that

    1 - you have indeed abandoned any notion of complex irreducibility of photosynthesis as untenable,

    2- you have now shifted your target and you are now addressing the complex irreducibility of ATP Synthase which photosynthesis co-opted from respiration.

    I would be happy to proceed with the complex irreducibility of ATP Synthase once you have addressed those two details.

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  16. Tom

    Before going to bed last night - I noticed you posed a question regarding the irreducible complexity of (OEC) involved in the photooxidation during photosynthesis.

    I seems to have vanished.

    True. Larry works in misterious ways.....

    1. You are right. If we apply the term in a strict way as coined by Behe, Photosynthesis as a whole is not irreducible complex, since its not composed by " well-matched, interacting parts ". Robert Blankenship described it, as " a very complex set of interdependent metabolic pathways ". Its irrelevant as Larry did, to claim there are simpler versions of photosynthesis. These versions do not keep the same function. In order to produce oxygen, the OEC is indispensable and irreducible, and , as i show in my study, any mutant of the proteins that constitute the OEC complex,make the function of oxygen production defective or impossible. These proteins could not emerge in a stepwise fashion, since they are if not working properly and in concert with all other parts, useless. And since they are uniquely used in OEC, they could either be co-opted.

    Oxygenic photosynthesis imho IS composed as well of several indispensable protein complexes. A particulary interesting case study is one of the most complex proteins known in nature, the Photosystem II complex. There are two issues that are unsurmountable problems for proponents of evolution to explain.

    In order to assemble PSII, assembly factors are required. Assembly of PSII is highly co-ordinated and proceeds through a number of distinct assembly intermediates. Associated with these assembly complexes are proteins that are not found in the final functional PSII complex. These are Ycf48/Hcf136, Psb27 and Psb28. They have no function by their own.

    Imagine a car factory. Robots mount the cars there, almost without any human intervention. All automatic. Like in a production line. Nano roboters ( the assembly factor proteins ) build the nano machines, like the PSII subunit, the oxygen evolving complex, ( which splits water utilizing energy from the sun to split water into protons, electrons and oxygen ) ,beside a large number of proteins, pigments, lipids and ions, in a highly coordenated and extremely precise, step-wise fashion. It proceeds through a number of distinct assembly intermediates. And when the job is done , they go away, they are not part and component of fully assembled monomeric and dimeric core complexes.



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    Replies
    1. True. Larry works in misterious ways.....

      No he doesn't.

      I will delete all your posts that are simply cut-and-paste jobs from your forum with no attribution to the original source.

      You are spamming my blog and that's not acceptable. Deal with the issues like an adult.

      Delete
    2. Otangelo Grasso

      Thank you for your patience and your indulgence. I find the thought processes behind your rationale intriguing and I congratulate you for your public courage in this lions’ den (as it were) and sharing with us the conviction of your beliefs.

      That all said, you clearly display some confusion and I am convinced any high school student should be able to dismantle your thesis. Let’s see if I can do this myself by restricting myself ONLY to what specifically has been my own students at a high school level.

      In your original OP you were not addressing photosynthesis per se but rather events restricted to the ETC of the inner membrane, where you claimed that:

      OG So, photosynthesis is a interdependent system, that could not have evolved, since
      [1]… all parts had to be in place right from the beginning.
      [2]… It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts.


      From what I can gather, you have pretended to retreat from that claim and have also moved the goal posts.

      OG You are right. If we apply the term in a strict way as coined by Behe, Photosynthesis as a whole is not irreducible complex, since its not composed by " well-matched, interacting parts ".

      Let’s deal with [2] since it is the easiest. As I already mentioned above, my high school students would be able to contradict you by observing:

      The events occurring in the inner membrane are NOT “irreducibly complex” and can be basically broken down into two complementary events:

      1 - events leading to the generation of useful ATP (photosystem II) and

      2 - events leading to the generation of useful NADP (photosystem I)


      I think we can both agree that ANY independent generation of either ATP or NADP is NOT “useless”

      Moving on to [1]… You then shift your argument (and I believe you are being sincere and earnest and not dishonest) by seeming to persist in wanting your cake and eating it too.

      You seem to want to again rescue the irreducible complexity of photosynthesis “as a whole” by claiming various individual components are uniquely irreducibly complex. So far you seem to have offered three candidates: P II, ATP Synthase, and OEC

      If I understand you correctly, the latter plays two essential roles in your thesis: OEC is in and of itself irreducibly complex and not only that; OEC’s role in photosynthesis is somehow so crucial to photosynthesis “as a whole” [disingenuous sneak through the back door!] that photosynthesis could NOT emerge by evolution, at least not according to mechanisms scientists currently understand.

      Why not?

      You state:

      Its irrelevant as Larry did, to claim there are simpler versions of photosynthesis. These versions do not keep the same function.

      Oh boy… my students would have fun with that! Where to start? How about the imperfection and poor design of homologous structures or co-opted structures. A reminder of the Panda’s Thumb would be a propos.

      Delete
    3. Otangelo Grasso

      Your next thesis is subtler and somewhat more sophisticated.

      .In order to assemble PSII, [similarly P II & OEC] assembly factors are required. Assembly of PSII is highly co-ordinated and proceeds through a number of distinct assembly intermediates. Associated with these assembly complexes are proteins that are not found in the final functional PSII complex. These are Ycf48/Hcf136, Psb27 and Psb28. They have no function by their own. .

      This is your strongest argument, but far removed from your original thesis by a long shot!

      Now this is indeed interesting and presents a challenge. I did say at the outset that I was to restrict my rebuttal to a level that could be provided by high school students according to what they learned in class.

      My students have learned about quaternary structure of proteins. Cases in point would include Hemoglobin, DNA binding proteins, various enzymes, and Plasma Membrane Receptors where the final functional structures included two or more protein subunits.

      The comparison of Myoglobin to Hemoglobin is a no brainer.

      Your challenge has been beneficial to me! In future I will need to dedicate more effort to biochemical evolution. I did mention in class how after gene duplication mutant versions two subunits with independent function could combine to create a new complex with a new function.

      Certain Enzyme complexes for example.

      I will need to expand my presentation in class to (briefly and in broad strokes) include specific examples such as
      - ATP Synthase and its commonalities with a DNA helicase with ATPase activity and H+
      motors of Flagella
      - or how the OEC resembles two catalase enzymes lashed together
      - or how seemingly irreducibly complex structures such as P II can be shown to have evolved in stepwise modular fashion.

      I will come up with some worksheet (at a high school level) based on what you generously have provided and will share it with my colleagues,

      I will send you a copy when I am done.

      In return and by way of parting gift, may I draw to your attention how Nick Lane slays your OEC shibboleth

      http://tinyurl.com/zepzaog

      I remain in your debt. I thank you and my future students thank you, for this opportunity to make me a better teacher.

      And while I am at it: again and as always, thanks as well to sandwalk.blogspot !

      Best regards to one and all

      Delete
    4. Tom

      The system i claim to be IC is photosynthesis, producing O2 and glucose . I am not retracting that all 26 mentioned proteins in the OP are required to produce O2 and glucose. A simpler system does not keep the function of O2 production. The only thing i grant is that if the characterization of a IC system is that it is " composed of several well-matched, interacting parts ", then this characterization might not apply to the photosynthetic pathway. Its better described as a INTERDEPENDENT system. Which does not take anything from my argument that photosynthesis is best explained through the intervention and creation of a intelligent designer.

      You wrote:

      How about the imperfection and poor design of homologous structures or co-opted structures.

      Whats with them ? What are you referring to ?

      Delete
    5. Otangelo,

      "Its better described as a INTERDEPENDENT system. Which does not take anything from my argument that photosynthesis is best explained through the intervention and creation of a intelligent designer."

      You don't have an argument here, because you have presented no evidence that the intervention and creation of an ID is needed. You have provided only arguments from ignorance.

      Delete
    6. Otangelo Grasso

      There is much confusion in what you post :

      I am not retracting that all 26 mentioned proteins in the OP are required to produce O2 and glucose.

      Oxygen is produced in the ETC (where Glucose is not produced) and in the Calvin Cycle (where Glucose is produced). Your sudden jump to the Calvin Cycle is not justified in your original incarnation of an IC thesis.

      In any case, neither instance of O2 production exemplifies IC, as has been already indicated above.

      One reason you are subject to so much rudeness would be your own impoliteness.

      If you are refuted – you should acknowledge as much.

      If in fact you feel you have not been refuted, you should also indicate as such (and why) before jumping (i.e moving the goalpost) to another topic.

      To do otherwise (as is your habit) is most impolite and worthy of a rude response.

      Delete
    7. Tom

      according to Wiki:

      Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy that can be later released to fuel the organisms' activities (energy transformation). This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesisk.

      The light dependent, and the light independent reactions are included.

      I did not expect that this would be reason of confusion of some sort.

      Delete
    8. Hi Otangelo

      My apologies – I was guilty of a brain-fart and realize now my error in incorrectly recalling the Ruben and Kamen 1941 experiment

      Two points –

      1 – I should have quickly written down the total equation for photosynthesis before answering you and not relied on brute memory

      2 - the 1941 Ruben and Kamen experiment is somewhat beyond what is required for students in high school although I do mention it very briefly when presenting the overall equation.

      6 CO2 + 12 H2O --> C6H12O6 + 6 O2 + 6 H2O

      Actually I also mention the evolutionary implications of the production of PGAL in chloroplasts proceeding production of Glucose or Ribose in the cytoplasm, but we digress.

      Bottom line - the reduction of Carbon Dioxide in the Calvin Cycle generates water and not Oxygen. I promise you I do a better job in class than I just did here.

      In any case, you were most disingenuous in your selective citation of wiki, because wiki goes on to explain the so-called “Light-dependent reactions” of Water photolysis and then goes on to explain the poorly named “Light-independent reactions”

      To continue with you wiki citation:

      Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy [Light-dependent reactions] … This chemical energy is stored in carbohydrate molecules [Light-independent reactions]

      Your whole IC thesis makes no mention of the Calvin Cycle and poorly named “Light-independent reactions” and you seem to betray much confusion by conflating the two processes of photosynthesis when your whole thesis revolves about that one diagram which focuses exclusively on events taking place in the inner Thylakoid membrane.

      Delete
    9. @Tom Mueller

      Only a small percentage of the chemical energy (ATP and NADPH) produced by photosynthesis in cyanobacteria and algae is stored in carbohydrates. Much of it is used in other metabolic reactions, including protein synthesis. How does that fact fit into your equation for photosynthesis?

      The idea that photosynthesis is coupled to the Calvin cycle is a very narrow perspective derived from looking only at photosynthesis in flowering plants. It's better ti teach bacterial photosynthesis first then show how it evolved into the more complex process in cyanobacteria and, later on, plant chloroplasts.

      When you do it that way, it becomes obvious that the capture of light energy to produce sucrose and other carbohydrates is a highly specialized phenomenon that's not really part of photosynthesis.

      I think it's important to teach biochemistry from an evolutionary perspective and it's important to teach students that there's more to life than just flowering plants and humans. The same strategy applies to teaching the rest of biochemistry from simple pathways to more complex pathways avoiding the impression that what we see in humans (e.g. glycolysis) is standard.

      Delete
    10. Hi Larry,

      Forehead-palm-slap to forehead! Yet again I need to thank you and yet again I will be sharing your insights on the AP Biology teachers’ forum.

      Yet again I am in your debt and I thank you!

      You are most correct and I share your sentiment:

      LM:
      I think it's important to teach biochemistry from an evolutionary perspective and it's important to teach students that there's more to life than just flowering plants and humans.


      AMEN!

      That would be my greatest criticism of the current incarnation of the AP Bio curriculum as it stands right now. Too much latitude is provided teachers by way of choice of illustrative example that permits teachers to do just that – restrict all of AP Biology to just flowering plants and humans.

      I have had my knuckles publically wrapped on the AP teachers’ forum, on more than one occasion, for pressing just that point (with perhaps too much enthusiasm).

      In my defense, I was responding to Otangelo Grasso’s oversimplification above where he did state that:

      OG: Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy that can be later released to fuel the organisms' activities (energy transformation). This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesisk.

      You will note my several contradictions of Otangelo including where I mentioned above that

      TM: The events occurring in the inner membrane are NOT “irreducibly complex” and can be basically broken down into two complementary events:

      1 - events leading to the generation of useful ATP (photosystem II) and

      2 - events leading to the generation of useful NADP (photosystem I)

      I think we can both agree that ANY independent generation of either ATP or NADP is NOT “useless”


      But your point IS STILL WELL TAKEN and I am delighted you took the time and effort to correct my naiveté.

      Thank you!

      Delete
    11. Here is the state of current approach currently taken by most high school curricula:

      The shelf-life (half-life) of ATP in solution is so short that Nature evolved out of necessity some mechanism to “store” or cache the energy captured by Water photolysis.

      Of course this is incorrect.

      In my perhaps only somewhat relatively less naïve version of events, I once suggested that that ATP cannot be stored; because storing such quantities of ATP would make it impossible to keep a cell isotonic with interstitial fluid unless Plant fluids had the same tonicity as syrup. Meanwhile, autotrophs that are exclusively dependent on Water photolysis need some mechanism to store energy as surely as night follows day if for no other reason that photosynthesis cannot occur in the dark. Of course, standard focus on extremely high human ATP requirements again skews any evolutionary appreciation of glycolysis (as you correctly point out). (parenthetically, and in all fairness, Nick Lane’s book Vital Question is causing a stir in AP Bio teacher circles.)

      Another textbook misconception (that you corrected on our very first email exchange) would be the error that NADH is exclusive to mitochondria and NADPH is exclusive to chloroplasts.

      This all would explain my grateful forehead-palm-slap upon reading your response.

      So to continue your challenging question to me – photoautotrophy evolved. Let’s see if we can confound Otangelo Grasso even further while keeping this to a level that high school students can easily grasp.

      LUCA was a chemoautotroph. Photo-autotrophy evolved as a later-on and in stepwise fashion. OEC clearly had abiotic origins and was co-opted as an oxidizing agent of water while simultaneously enabling the transfer of higher energy electrons to pre-existing electron carriers. In other words, Photo-autotrophy was an evolutionary tag-on to chemoautotrophs where the very first photoautotrophs were facultative photoautotrophs that supplemented chemoautotrophy.

      Actually, I mention facultative photoautotrophy in class in passing, but so far have restricted such mention to organisms that alternate between photoautotrophy and chemoheterotrophy. Off the top of my head, I am unaware of any modern organism that alternates between photoautotrophy and chemoautotrophy.

      In any case, I will alert my colleagues to this very informative thread and highlight your imperative to teach biochemistry from an evolutionary perspective and to expand consideration of illustrative examples to more than just than just flowering plants and humans and that that the capture of light energy to produce sucrose and other carbohydrates is a highly specialized phenomenon that's not really part of photosynthesis… although I suspect that last bit will furrow more than a few foreheads!

      Delete
    12. I once suggested that that ATP cannot be stored; because storing such quantities of ATP would make it impossible to keep a cell isotonic with interstitial fluid

      ATP hydrolysis and synthesis are equilibrium reactions like all other reaction inside the cell. Cells must maintain a high concentration of ATP relative to ADP in order to benefit from the free energy change of hydrolysis.

      If a cell were to "store" ATP molecules then the steady-state concentrations would change significantly. There would be two serious effects.

      1. The increase in the Gibbs free energy of hydrolysis due to higher concentrations of ATP (relative to ADP) would mean that spontaneous hydrolysis would become a serious problem.

      2. The big increase in the positive ΔG for synthesis of ATP would make it impossible for ATP synthetase to make any ATP against the concentration gradient.

      All living cells "store energy" in the form of glycogen. This includes all those species that are incapable of photosynthesis and many that are. Don't forget that the role of glycogen as an energy storehouse predates photosynthesis and has nothing to do with "water photolysis."

      The fact that plants make starch instead of glycogen is irrelevant. It's a derived feature.

      And don't forget that the product of the Calvin cycle is glyceraldehyde-3-phosphate and not glucose, sucrose, or starch. G3P is used in all kinds of pathways such as making amino acids and nuleotides. It's not just used for storing energy by acting as a precursor to glucose and glucogen/starch. So claiming that the overall equation for photosynthesis is production of a 6-carbon sugar is misleading in more ways than one.

      Delete
    13. @ Larry Moran

      ;-) It is a good thing I preemptively opened with:

      In my perhaps only somewhat relatively less naïve version of events…

      I think that I am not incorrect that viscosity would become an issue at some point, but of course, your explanation kicks in long before mine would:

      LM:

      1. The increase in the Gibbs free energy of hydrolysis due to higher concentrations of ATP (relative to ADP) would mean that spontaneous hydrolysis would become a serious problem.

      2. The big increase in the positive ΔG for synthesis of ATP would make it impossible for ATP synthetase to make any ATP against the concentration gradient.


      This would be the second time today that I did a forehead-palm-slap!

      Of course! High School Bio students can understand this explanation – at least those at an AP level. So why is this the first time I have ever seen this explanation!!!

      Again, I remain in your debt and I thank you!

      Regarding your second point:

      LM:

      And don't forget that the product of the Calvin cycle is glyceraldehyde-3-phosphate and not glucose, sucrose, or starch. G3P is used in all kinds of pathways such as making amino acids and nuleotides. It's not just used for storing energy by acting as a precursor to glucose and glucogen/starch. So claiming that the overall equation for photosynthesis is production of a 6-carbon sugar is misleading in more ways than one.


      In fact - I do cover this in class at the level you describe. I refer you to my answer to

      TM:
      Actually I also mention the evolutionary implications of the production of PGAL
      [for the benefit of Otangelo, PGAL is another acronym for G3P] in chloroplasts proceeding production of Glucose or Ribose in the cytoplasm, but we digress.

      Found on http://tinyurl.com/h4hrh47

      Otangelo Grasso was clearly in over his head and I did not want to overwhelm more than he already was. I was hoping against hope he would address the refutations he already had failed to address without adding any more.

      I find Otangelo Grasso’s intellectual dishonesty quite disappointing.

      While I am here, I need to thank you for your post http://tinyurl.com/ztze6pf


      I never stopped to think that

      1 – cynaobacteria are NOT at all ancient (in relative terms)
      2 - most other photosynthetic bacteria such as purple bacteria do NOT produce oxygen

      Again – introductory textbooks are most delinquent on this subject and you have caused me to undergo a complete rethink on the topic.

      Thank you.

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    14. @ Larry Moran

      I think I may do some of my best editing after I hit "SEND"

      I realize that the catch-all term "photosynthesis" is misused/abused.

      As you have made abundantly clear, there are many versions of the oxidative photolysis of water that captures and converts light energy into chemical energy without continuing to the synthesis of Glucose/Starch.

      In order to parse our words more carefully, would you recommend teachers explicitly employ the term "photosynthesis" ONLY when PGAL/G3P is in fact being manufactured; all the while emphasizing that the majority of the time, the electron-carriers ATP and NADPH are in fact diverted for other anabolic processes.

      If so, what should we call this generic process of "...oxidative photolysis of water that captures and converts light energy into chemical energy for a variety of purposes"?

      Delete
    15. Tom
      "I realize that the catch-all term "photosynthesis" is misused/abused.
      As you have made abundantly clear, there are many versions of the oxidative photolysis of water that captures and converts light energy into chemical energy without continuing to the synthesis of Glucose/Starch"

      I think you and Larry have made a good case the polarizing statement that photosynthesis could not have evolved is a stretch. Do you have a case how it might have evolved and the mechanism involved .

      Delete
    16. @ Bill Cole

      I am not sure what you mean by "it"

      As far as I can make out, I think Larry already answered your question here:

      http://tinyurl.com/ztze6pf

      Delete
    17. Hi Tom
      By it I mean the evolution of photosynthesis in plants. How did the genome change over time to perform the precise photosynthetic mechanism we see today? Was it population genetics, natural selection, HGT, random mutation, exon shuffling, splicing code modifications?

      Delete
    18. This comment has been removed by a blog administrator.

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    19. Tom Meuller asks,

      If so, what should we call this generic process of "...oxidative photolysis of water that captures and converts light energy into chemical energy for a variety of purposes"?

      That would be one version of photosynthesis—the version that's found in cyanobacteria, algae, and plants. Other versions don't use water as an electron donor. The oxidative photolysis of water is not necessary for photosynthesis.

      The chemical energy that's produced is NADPH/NADH and ATP, not G3P or any other carbohydrate.

      Delete
    20. Larry wrote:

      Their dual photosystems clearly evolved late from a combination of a type I reaction center in species like Heliobacter and green sulfur bacteria and a type II reaction center from species like purple bacteria and green filamentous bacteria.

      Please explain why you say " clearly evolved ". As you know, i have not the " If Larry just says so, it must be true " attitude. If you make such a assertion, you need to back up your claim. Most welcome, if you could expose also the details, how exactly it supposedly happen, in order for you to come to your supposedly clear conclusion.

      And since we are at cyanobacteria. I cite from my library:

      http://reasonandscience.heavenforum.org/t1551-cyanobacteria#2319

      If there was a reduced atmosphere without oxygen some time back in the past ( which is btw quite controversial ) then there would be no ozone layer, and if there was no ozone layer the ultraviolet radiation would penetrate the atmosphere and would destroy the amino acids as soon as they were formed. If the Cyanobacterias however would overcome that problem ( its supposed the bacterias in the early earth lived in the water, but that would draw other unsurmountable problems ), and evolve photosynthesis, they would have to evolve at the same time protective enzymes that prevented them oxygen to damage their DNA through hydroxyl radicals. So what evolutionary advantage would there be they to do this ?

      Nick Lane describes the dilemma in the book Oxygen, the molecule that made the world:
      Before cells could commit to oxygenic photosynthesis, they must have learnt to deal with its toxic waste, or they would surely have been killed, as modern anaerobes are today. But how could they adapt to oxygen if they were not yet producing it? An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favour such a catastrophic history. In terms of the traditional account of life on our planet, the difficulty and investment required to split water and produce oxygen is a Darwinian paradox.

      They have ATP synthase nano-motors. How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function?

      Delete
    21. Was it population genetics, natural selection, HGT, random mutation, exon shuffling, splicing code modifications?

      Yes.

      Delete
    22. Oh yeah, sure....

      almost forgot to ask.

      How do you possibly know ?

      Delete
    23. An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favour such a catastrophic history.

      Um... Banded Iron formations. Photosynthetic cyanobacteria would increase in number, leading to rising oxygen levels, which would lead to the collapse of most of the population. The Oxygen would weather iron rich minerals and thus its concentration would sink (leaving sediment enriched in iron oxides). When the levels were low enough again, the population size of the Cyanobacteria would spike again. During the low Oxygen periods the sediments would not contain a lot of iron oxides. And do we find this cycle of iron rich sediments and iron poor sediments? Right at the time where we think photosynthesis got going? We do indeed.

      Delete
    24. @Larry Moran

      Let's see if I can do this with sore thumbs on a iPhone:

      LM: "The chemical energy that's produced is NADPH/NADH and ATP, not G3P or any other carbohydrate."

      That was exactly what I said (and even tried to explain to OG on more than one occasion) and in fact the premise of my question. Let's see if I can parse my words more precisely... For the benefit of high school students and in order to prevent confusion, most of what happens in the chloroplast ETC ( even in flowering plants ) is not directed to the Calvin Cycle. That is why I asked whether it may be a good idea to come up with some new generic label for the events occurring within a chloroplast, given nomenclature can be misleading, as misleading as say "light independent reactions" which too is a misnomer.

      LM: "That would be one version of photosynthesis—the version that's found in cyanobacteria, algae, and plants. Other versions don't use water as an electron donor. The oxidative photolysis of water is not necessary for photosynthesis. "

      Again I apologize for not parsing my words more carefully.
      Again understood, as I immediately above said the very same thing:

      TM:- "...most other photosynthetic bacteria such as purple bacteria do NOT produce oxygen"

      Again, to reiterate my question: is it fair to suggest the catch-all term "photosynthesis" is too encompassing, leads to misconception, and needs replacement?

      I do not see this happening soon. In class I alert my students to events in the stroma often being labeled "light independent" and explain why that is not really the case.

      I was thinking of taking a similar approach with events that occur in the chloroplast and coming up with a better generic name than "photosynthesis"

      ITMT I am humbled and chagrined to think my approach all these years past could have been much better. By neglecting to cite various instances of conversion of light energy to chemical energy in bacteria in evolutionary terms, I have failed my students.

      Again, I remain in your debt and thank you.

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    25. How do you possibly know?

      If you understood the least thing about biology, how could you possibly *not* know?

      The question essentially asked whether, over an enormous span of time, the same processes we see going on every day in all life on Earth went on then. The answer obviously is yes, unless all these fundamental life processes simultaneously decided to take a hundred million year vacation, for which there is utterly no evidence whatever.

      Delete
    26. @ Larry Moran

      Now that I am sitting in front of a computer and no longer relying on an iPhone, it is easier for me to identify where our exchange fortuitously derailed.

      I was in fact responding to OG's confused citation from wiki where he in fact was guilty of conflation and I was attempting to correct him…
      http://tinyurl.com/jlhoybw

      I could have chosen my words better. Still our derailment was fortuitous, because you have provided me some excellent sound-bites that permit ready and easy quotation.

      ITMT, I have been giving this some more thought on how best to explain this to my colleagues and I think I may have identified where a major conceptual trap may lie.

      Introductory Biology spends a lot of time on Ecology and discussion of trophic levels. The issue becomes one of semantics where consideration of photosynthesis by “producers” to generate the “Biomass” for higher Trophic Levels can possibly lead thinking astray.

      A rethink should include further consideration that

      1 – Plants can divert PGAL/G3P to other biochemical pathways other than creation of Glucose/Starch when generating “Biomass”

      2 – Plants not only can but (in fact most of the time do) decouple ATP/NADPH production from Carbon fixation. Much of the ATP & NADPH generated by Photosystems II & I respectively are in fact redirected to immediate energy needs, even in flowering plants.

      IOW, I think that some persistent fuzziness in thinking is in small part due to a conflation of photosynthesis with generation of Biomass which itself becomes conflated with generation of Glucose/Starch/Cellulose

      I checked out a relevant Wikipedia article:

      https://en.wikipedia.org/wiki/Photosynthetic_efficiency

      100% sunlight → non-bioavailable photons waste is 47%, leaving
      53% (in the 400–700 nm range) → 30% of photons are lost due to incomplete absorption, leaving
      37% (absorbed photon energy) → 24% is lost due to wavelength-mismatch degradation to 700 nm energy, leaving
      28.2% (sunlight energy collected by chlorophyll) → 32% efficient conversion of ATP and NADPH to d-glucose, leaving
      9% (collected as sugar) → 35–40% of sugar is recycled/consumed by the leaf in dark and photo-respiration, leaving
      5.4% net leaf efficiency.


      Of course, this still leaves unaddressed your other salient insight that

      LM: …It's better to teach bacterial photosynthesis first then show how it evolved into the more complex process in cyanobacteria and, later on, plant chloroplasts.

      AMEN!...which I will address in more detail below.


      Bottom Line: from now on in class, I shall be certain parse my terms far more carefully and be sure to mention “nonphotosynthetic photophosphorylation” in evolutionary terms as distinct from “photosynthesis”.

      Again and as always I remain in your debt!

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  17. This comment has been removed by a blog administrator.

    ReplyDelete
    Replies
    1. The whole blather there is one large argument from ignorance. Yes, I know you will now bring some copy-paste apologetics that claims it isn't an argument from ignorance. But it IS an argument from ignorance. It is an argument from ignorance when you are trying to claim Intelligent Design isn't just more likely, but that evolution is impossible - because everything isn't known about PSII evolution. You consistently claim that evolution isn't just unknown or unlikely, but that it is impossible.

      An argument from ignorance is actually a type of non-sequitur fallacy. Non-sequitur: It doesn't follow.
      It means the conclusion doesn't follow from the premise. It doesn't follow that PSII cannot and did not evolve, just because there might be significant areas of ignorance regarding it's history. It doesn't follow that we should believe PSII was intelligently designed, just because there might be significant areas of ignorance regarding it's history.

      K does not currently explain P, therefore K will not ever explain P. Non-sequitur.
      There are no known versions of K that explain P, therefore K should be discarded in favor of K2. Non-sequitur.
      We do not know k part of K which is necessary to account for P, therefore not-K. Non-sequitur.

      There's another flaw in your attemtp to "infer" whether something is designed or not, which is that there is zero actual evidence for a biological structure being designed. You have to have an actual reason to think there's a designer of life, as in an observation of the designer at work. We only know of two designers: Humans and Evolution. But we know that humans didn't design life.
      Evolution is an observed process, we can prove it happens right now. But nowhere is there any indication that biological organisms are being continously "designed" and poofed magically into existence. It just doesn't happen. Additionally ID makes no testable predictons, it is all ad-hoc. For the systems where we DO know in great detail how they came about, we know they evolved and weren't designed. So even if you managed to prove that some particular biological structure could not possibly evolve through currently understood means you would still have all your work still ahead of you. You would still have to actually show that it was and how it was designed. You don't accomplish that by arguing the current theory of evolution hasn't done so (yet).

      Delete
    2. "Why would evolution produce assembly factors, if assembly is only required when there is actually something to be assembled ?"

      Maybe they were part of something else before? How do you know?

      Delete
    3. Otangelo:
      I did not shift any target. ATP synthase is a integral part of photosynthesis, thats why i mentioned it.

      a post above you wrote:

      You are right. If we apply the term in a strict way as coined by Behe, Photosynthesis as a whole is not irreducible complex,

      So yes, you are moving the goalposts, because your original position which is: Photosynthesis is OEC. And you admit it yourself, it isn't.
      So you shift the goalposts to ATP synthase.

      Furthermore, you repeat the same 'arguments and analogues' about how OEC ATP synthase is, 'arguments and analogues' which less than a day ago you also applied to Photosynthesis. Which you just admit isn't OEC.

      And along the way you open the option to shift the goalposts again to the Photosystem II complex.
      Once again, you claim stuff but you are lacking any evidence what so ever to support your claims. Just a mention:
      In order to produce oxygen, the OEC is indispensable and irreducible, and , as i show in my study, any mutant of the proteins

      Which study?

      Anyway, Gish would've been proud of you.

      Delete
    4. Rumraket

      my argument is entirely based on WHAT WE DO KNOW. No argument from ignorance here.

      The key process that produces oxygen in the atmosphere is due to the oxygen-evolving complex (OEC) , which splits water molecules and subsequently releases molecular oxygen. This process, which occurs in photosystem II (PSII), is driven by the conversion of visible light to chemical energy. Electrons oxidize water, which leads to the evolution of molecular oxygen and the release of protons into the thylakoid lumen. This proton gradient is a major contributor to the proton motive force used to biosynthesize ATP from ADP via ATP synthase.

      The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In plants there are four (PsbO, PsbP, PsbQ and PsbR). Maintenance of the highly dynamic Mn4CaO5 cluster also requires the delivery of a constant supply of the proper levels of Mn2+ and Ca2+. The mechanism of water oxidation has remained virtually unchanged between green plants and cyanobacteria, and is similar in all higher plants. Simpler mechanisms are unknown.

      Each of the extrinsic proteins of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient, and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster, and D1 protein subunit of PSII are also absolutely necessary. Each protein and the Mn4CaO5 cluster has no function by its own, only, if duly embedded and working in the whole mechanism. It could therefore not provide any survival advantage to the organism, unless everything is set up. Its the same as to ask what good a piston motor would be by its own ? It has no function , unless duly mounted and well matched inside the motor block.

      There is no ignorance, but based on the scientific evidence of mutation experiments WE DO KNOW OEC absolutely requires each protein and a precisely arranged Mn4CaO5 cluster fully evolved and set up.

      1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
      2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
      3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
      4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.

      Delete
    5. Plants lacking PsbQ show almost no effects under optimal conditions but they don't survive under low light conditions. This shows that PsbQ is NOT essential. Presumably, primitive plants got along without PsbQ by growing in the best places but the evolution of PsbQ allowed them to invade areas with less light.

      PsbR also seems to be dispensable under some environmental conditions. Plants can exhibit photoautotrophic with just PsbO in the absence of PsbP, PsbQ, and PsbR genes. There are effects on oxygen-evolving ability but these are quantitative—reduced efficiency—instead of qualitative all-or-none effects.

      Allahverdiyeva et al.(2013) Arabidopsis plants lacking PsbQ and PsbR subunits of the oxygen-evolving complex show altered PSII super-complex organization and short-term adaptive mechanisms. The Plant Journal 75: 671-684.

      Delete
    6. There is no ignorance, but based on the scientific evidence of mutation experiments WE DO KNOW OEC absolutely requires each protein and a precisely arranged Mn4CaO5 cluster fully evolved and set up.

      Actually, there's a great deal of ignorance on display here.

      Delete
    7. Hence the rule: "The rule of thumb with Otangelo is: Everything he says is diametrically opposite to demonstrable fact." - Me

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    9. Mikkel

      please school me.

      Show a simpler version of oxygen producing photosynthesis . and how it evolved to what we have today. What came first, the assembly factors of PSII, or PSII ? the repair mechanism of D1 subunit, or the D1 subunit ? And how was the assembly process and sequence, and repair sequence programmed ? trial and error ?

      Delete
    10. Oh look, more arguments from ignorance. Propped up with a hypocritical request for details you can't provide yourself.

      Hypocrite.

      Delete
    11. yep.

      So no answer ? thought so....... haha.

      Btw. My answer to your question about the design process was deleted by Larry.

      Which keeps doing a terrible, aweful job as moderator, vandalizing and deleting posts without or lame excuses.

      But you are a good pupill of Larry, Mikkel. Both of you replace scientific reasoning and rational inferences with name calling and mocking of design proponents. No wonder, are there not many ID proponents showing up here.....

      Delete
    12. I keep being surprised that you allow yourself to type out these counterfactual rants all the time. We keep explaining logic to you, because underlying all your problems is ignorance of basic logic which leads you to make so many invalid inferences and deductions.

      Rather than have endless debates about evidence with you, you must first learn to think correctly. I don't know how to keep coming up with new and inventive ways to explain what basic fallacies are and how to avoid them.

      You keep bringing up Irreducible Complexity in arguments that are either outright deductively invalid (they are non-sequiturs, the conclusion does not follow from the premises) or are simply based on faulty information (the premises are provably false).

      I don't know what else to do now. There doesn't seem to be any point to arguing about particular pieces of evidence and theory when your problem is much more basic. When people respond to you with mockery, it's not because they can't do anything else, it's out of exhasperation that after so much time, you still fail at the most basic level of discourse: Thought itself.

      Take an example, further down in this thread you write: "A simpler version of oxygen producing photosynthesis would only exist, if it would keep the function of producing oxygen."

      Isn't it trivial to see the error in reasoning you make here? It is to me. Maybe, juuuuuuust maybe, the simpler version of photosynthesis did not produce oxygen, then?

      The "function" of photosynthesis is not to produce oxygen, it is to power chemical reactions. Oxygen is just a waste product, and chemical reactions can be powered by light with waste products other than oxygen.

      So there you go, your "argument" committed an elementary error in reasoning AND it was based on faulty information.

      Delete
    13. Mikkel

      you seem to live on the moon, detached from reality. Take note and check the evidence i have exposed, and why i infer design as the best explanation, and how many of these logical inferences you were able to refute with more compelling naturalistic explanations. Know how many ? NONE.

      " We keep explaining logic"

      Are you of a Kings importance to refer to yourelf in the plural ? Or is it just your blown ego, which the less justified your world view is, the more you blow it to compensate the emptyness ?!!

      How about rather than make lunatic acusations, you actually demonstrate where my logic fails ?

      "(the premises are provably false)".

      You are kidding me, right ? Show me ONE premise of mine e which was demonstrably false. Just one.

      " It is to me. Maybe, juuuuuuust maybe, the simpler version of photosynthesis did not produce oxygen, then? "

      hahahahaha. You are kidding, right ? My sentence is perfectly logical and valid, and TRUE. THERE IS NO KNOWN SIMPLER PATHWAY OF OXYGENIC PHOTOSYNTHESIS KNOWN.

      There are simpler versions of photosynthesis, which imho DO NOT PRODUCE OXYGEN. That was my entire point by which i refuted Larrys claim, that photosynthesis is reducible. Its not , if oxygen production is kept. If oxygen is a waste product or not, is irrelevant to the case. Its this waste product that makes you be here and write foolishness.

      Delete
    14. Well, I suppose it is true that there is no form of oxygenic photosynthesis that does not make oxygen, just as there are no tall dogs who are not tall. However, there are forms of photosynthesis that don't make oxygen, just as there are dogs that are short.

      Delete
    15. bwilson:

      " Well, I suppose it is true that there is no form of oxygenic photosynthesis that does not make oxygen ".

      It is true that there is no form of simpler pathway of photosynthesis that produces oxygen, than the one we know of.

      Mikkel: " Ladies and gentlemen, I rest my case. "

      You had a case ? What case ?! kk.

      Delete
    16. "You had a case ? What case ?! kk."

      No scientific response to Mikkel? How sad.

      You haven't even completed the first step of your goal to show that IC systems are impossible to evolve through natural processes. Mikkel is right, your flaw is very basic. Take your first baby step, and provide one piece of positive evidence for intelligent design.

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    17. @ bwilson295

      In order to understand photosynthesis in evolutionary terms; many prokaryotes, including both Bacteria and Archaea employ light-driven photophosphorylation to convert light energy into chemical energy, and not for the building of any biological molecules.

      As you already teach your undergrads, a vestige of these “primitive systems” systems persists even still in so-called “higher plants” in a process called “cyclic photophosphorylation” where P I generates ATP for the immediate energy needs of the plant.

      Electrons are recycled back to P I without generating NADPH.

      Interestingly, the electrons transferred are not derived from water, but from P I itself, explaining why they must be recycled to P I, a mechanism that plants inherited from a common ancestor shared with extreme halophilic Archaea. That would conclusively slay the shibboleth of photosynthesis as Irreducibly Complex.

      Would this constitute a "form of oxygenic photosynthesis that does not make oxygen " ?

      ;-)

      Delete
  18. This comment has been removed by a blog administrator.

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    Replies
    1. Otangel Grasso posted a link to his forum where he claimed that what he posted was "his study." In fact it was plagiarized from an article by Jennifer Lockhart published on April 6, 2016 in the journal The Plant Cell.

      Delete
    2. Professor Moran

      the sources of the study i published at my virtual library, namely :

      The oxygen evolving complex (OEC) of photosystem II is irreducible complex

      are all mentioned at the end of the article. No plagiarism there.

      Please stop making false acusations.

      Thanks.

      Delete
    3. So, to be clear, you did not mention in the post you made here at Sandwalk that the passage you posted was quoted from another article?

      Delete
    4. One problem with Otangelo's copypasta is it often contains sentences and sections he wrote himself mixed in with the endless pasta. But he doesn't put copied material that isn't his own in quote tags or use any other kind of indicators that allow the reader to determine which are his own words and which are just quotemines. This gives the false impression the people he plagiarize support his conclusions.

      Of course, once you become familiar with him you quickly discover all the spelling, grammatical and logical errors in his work so you can see which parts he wrote himself.

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    5. Otangelo Grasso

      the sources of the study i published at my virtual library, ... are all mentioned at the end of the article. No plagiarism there.

      Please stop making false accusations.


      There's a big difference between referencing the source of your knowledge and inserting exact sentences into your article and claiming that it is your work.

      It's plagiarism when you copy and paste sentences and paragraphs without using quotation marks to show that these aren't your own words.

      Try doing that in a university course and see if you can avoid being given an F.

      Delete
    6. ok, i will try to be more careful to make it clear which are my writings, which are not.

      In the specific case in question however, you deleted a post where i only provided the title of my study, and the link.

      Delete
    7. Larry is right Otangelo.

      If you want to make a point on this forum, make sure your link is the right one-belonging to the "right authors".

      However, if you wish/would like to make a name for yourself, this is not your forum. I painfully have to sympathize with the "judge and the jury" even though I'm not on their side.

      On this blog, your reputation can and will be tarnished by ONE,even a minor mistake. Darwinists have the luxury of making many, many mistakes as they go along and then claiming that they had predicted those.

      You don't have that luxury! So, get your act together or stop posting shit!

      That's my advice...

      Delete
    8. Eric

      my name is irrelevant. And the participants have a great oportunity to provide good reasons why it makes sense to believe, photosynthesis evolved. Unfortunately, they have missed the chance. Its understandable , why. The attempt to critizise the messenger, rather than the message, is not a new tactic to distract from the real issue. Namely: Evolution is a irrational and impotent cause for biological complexity. This has been more than exposed at this topic. Goal reached.

      Delete
    9. God of the gaps argument, Otangelo. that's your argument, and it's as impotent as it has ever been. Goal not reached. Demonstrate IC systems cannot be produced by evolution, and you have taken your first baby step toward your goal.

      Delete
  19. This comment has been removed by the author.

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  20. In this case, Larry attempts a classic misdirection. Just like with the blood clotting system comparison between humans and lampreys.

    Larry wants us to believe that since a Lamprey has a simplified version of a human blood clotting system, it proves that the blood clotting system is not irreducible.

    Yet, we know that is not true. Why? Each blood clotting system is tailered to the organism. One is not the precursor of the other.

    This case is the same. Larry's pointing out that there is a simplified version of photosynthesis existing in some other organism does not provide one iota of evidence that the simplified version is a precursor of the more complex version.

    They are simply different versions of photosynthesis tailered to the individual organism's structure and needs.

    But Larry already knows this. He just has no better explanation since he's wedded to a non-teleological evolutionary narrative.

    He has no choice but to mislead and misdirect.

    So much for non-teleological evolutionary explanations.

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    Replies
    1. I think you're missing the point about irreducible complexity. It's primarily an attempt to prove the claim you are promoting. IDiots aren't comfortable just declaring that all species were created independently, as you do. Instead they want to provide actual "evidence" that irreducibly complex systems could not possibly have evolved.

      It's supposed to be a scientific argument, not a religious one.

      In order to refute that argument, all we need to do is show some plausible evoltionary pathway to an irreducibly complex system and/or show that it is not irreducibly complex.

      Once we've done that, the IDiots have to fall back on simple declarations of faith, as you have, and they've lost the scientific argument.

      Delete
    2. Each blood clotting system is tailered to the organism. One is not the precursor of the other.

      Since Michael Behe was utterly unable to prove this proposition, I find it unlikely in the extreme that Steve will. But have at it Steve - where's your proof?

      Delete
    3. Larry, I have not made a declaration of faith. It is simple logic.

      In fact, it appears that YOU are making a declaration of faith that since you can imagine an evolutionary pathway, then it most likely exists.

      So no, refuting the argument of irreducible complexity is not about showing some plausible pathway. It is actually demonstrating scientifically that in the ancetral hominid lineage, there was in fact a very simplified version of the human clotting system.

      You haven't done that. You show a lamprey with a simplified version of a clotting system, and leap to the assumption that earlier hominids just had to have some sort of simplified version of a clotting system similar to modern lampreys.

      That, im afraid is not science. It story-telling.

      Same with photsysthesis. show that the ancestors of a partucular plant has a simplified version of photosynthesis. To show that some randomly discovered organism happens to have what appears to be a simple photosynthesis mechanism says absolutely nothing about the evolutionary history of another organism.

      Design makes a whole lot more logical sense than non-teleological explanations.

      Just because you haven't the faintest idea how nature could adjust photosynthesis mechanisms to fit different organism's needs is not a reason to reject design.

      We already know nature designs. We just don't know YET how it does it.

      that is why 21~22nd century biology will be exciting. Sooner or later we will pry out nature's design toobox and methodology.

      It's just a matter of time.

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    4. I like it! We see less complex versions of the blood clotting cascade throughout the history of life, and so we should conclude from this *not* that the human system evolved from these less complex ones, but instead that all these similar systems are totally unrelated by descent; rather, that each and every one was specially created individually by a Divine... err, sorry, Designer. Because - why, because it's obvious, that's why!

      The fun never stops. :-)

      Delete
    5. Steve wrote, ". . . refuting the argument of irreducible complexity is not about showing some plausible pathway. It is actually demonstrating scientifically that in the ancestral hominid lineage, there was in fact a very simplified version of the human clotting system. . . . You show a lamprey with a simplified version of a clotting system, and leap to the assumption that earlier hominids just had to have some sort of simplified version of a clotting system"

      This is a case where not understanding evolution makes Steve unable to understand the argument being made. NOBODY thinks ancestral hominids had a simple blood clotting mechanism like that of lampreys. The idea is that the simple blood clotting system of lampreys shows that ancestral fish could, and did, survive with simple blood clotting systems. Some of those early fish were ancestors of fish that were ancestors of amphibians that were ancestors of synapsids that were ancestors of mammals that were ancestors of hominins including humans. Therefore, simple blood clotting systems could (and did) exist in the human lineage -- so far back that those ancestors were fish.

      Delete
    6. Wow. My ancestors were fish? What kind of potent product do you use for brain washing ?

      Delete
    7. Yes, our way way back ancestors were fish. You didn't know? I'll bet reading Neil Shubin's book "Your Inner Fish" would blow your mind. (It's all good biology.)

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    8. "Wow. My ancestors were fish? What kind of potent product do you use for brain washing ?"

      Beats the talking snake story.

      Delete
    9. Beats the talking snake story.

      Which in itself is quite a fish story!

      http://www.dictionary.com/browse/fish-story

      Delete
    10. B Wilson
      "Therefore, simple blood clotting systems could (and did) exist in the human lineage -- so far back that those ancestors were fish"

      Do you have evidence to support this claim?

      Delete
    11. BC -- There's abundant evidence to support the fact that our ancestors were fish. A couple good recent books covering this are "Why Evolution is True" and "Your Inner Fish," but there are many, at technical or beginner's levels. Go find out.

      Delete
    12. BW
      There's abundant evidence to support the fact that our ancestors were fish. A couple good recent books covering this are "Why Evolution is True" and "Your Inner Fish," but there are many, at technical or beginner's levels. Go find out."

      So your argument is based on the assumption Coyne etc is correct. Any experimental evidence?

      Delete
    13. No, BC. I recommend those books because I think they do a good, clear job of explaining evolution to non-biologists.

      I think evolution happens (and fish are among our ancestors) because over the past decades I have learned a lot about the patterns of present biodiversity and genetics. I have observed fossils, even collected a few, and read a lot about fossils and geology. I have even groaned through the math of population genetics, not enough to be good at it, but enough to see the logic. I've learned enough about genetics to teach it. I have read scientific papers on the evolution of various groups, and when those papers are important for research I'm interested in, I've looked for flaws in the selection or analysis of molecular markers, for example. I observe how the idea of evolution makes sense out of the patterns of plant diversity that I work with.

      As a result, I have a base of knowledge from which to judge whether "Why Evolution is True" and "Your Inner Fish" are, in general, accurate. I do not base my opinions on the assumption that Coyne or Shubin must be correct.

      Delete
    14. So your argument is based on the assumption Coyne etc is correct. Any experimental evidence?

      Yes. "Your Inner Fish" was written by Neil Shubin. The book describes in part his search for a fossil of a fish with particular evolutionary characteristics. Evolutionary biology and geology predicted the location at which such a fossil might be found. This prediction was confirmed by Dr. Shubin finding a fossil with the predicted characteristics in the predicted location.

      Unless evolutionary biology and geology were both correct, there would be no reason to find that particular fossil in that particular place. Thus the search for the fossil and the successful find constituted an experiment verifying the interacting predictions of these two sciences.

      Delete
    15. Judmarc, sometimes I wish the comments had a "like" button.

      Delete
    16. Judmarc

      " The book describes in part his search for a fossil of a fish with particular evolutionary characteristics. Evolutionary biology and geology predicted the location at which such a fossil might be found. "

      We read at :

      http://www.uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/

      In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight, or digestion, or immunity, must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance.

      The point which Professor Behe makes for vision applies equally to macroevolution as a whole. The relevant steps in macroevolutionary processes occur ultimately at the molecular level, so a satisfactory explanation of macroevolution must include a molecular explanation.

      If, for some reason, certain macroevolutionary transitions appear to be highly improbable from a chemical standpoint, then that in itself is a good reason to be skeptical of the view that Darwin’s theory of evolution is an all-inclusive theory of biology.

      Delete
    17. "The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step."

      You can't explain it through intelligent design. In fact, you have no plausible explanation at all. hiding behind ignorance leaves you unable to make any positive argument for your "alternative" to evolution. All of the details about complexity of biochemical reactions you cut and paste were all elucidated by scientists, using naturalistic scientific principles to gain knowledge. You can quote them all you want, but you still have not progressed the argument any further than: 'scientists cannot explain it all, therefore god'. Your argument ids the same as it always has been. You add nothing new to the discussion.

      Delete
    18. BW
      I think evolution happens (and fish are among our ancestors) because over the past decades I have learned a lot about the patterns of present biodiversity and genetics. I have observed fossils, even collected a few, and read a lot about fossils and geology. I have even groaned through the math of population genetics, not enough to be good at it, but enough to see the logic. I've learned enough about genetics to teach it. I have read scientific papers on the evolution of various groups, and when those papers are important for research I'm interested in, I've looked for flaws in the selection or analysis of molecular markers, for example. I observe how the idea of evolution makes sense out of the patterns of plant diversity that I work with. "
      Have you thought about how the genome of a fish becomes the genome of a human. What is the mechanism to get from A to Z. A being the genome of a fish and Z being the genome of a human. B through Y being the potential intermediates. The genome is mathematically a sequence, the largest mathematical space in the universe. What is the mechanism that transitions the genome from A to Z. In the book why evolution is true Jerry Coyne said that the theory was the best alternative explanation despite the problems. I think based on this, the best answer is we don't know vs some answer that is almost certainly wrong.

      Delete
    19. Fish genomes aren't part of my area of expertise. In the parts of biology I know about well, evolution theory seems to work well. Evolution also seems to explain the structural changes we see from early fish to tetrapods, etc. (Remember, structure is a result of genes, so it tells us something about genomes.) So I see good reason to think evolution theory is right. There's a lot more to learn about it, as there's a lot more to learn about most complicated thing.

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    21. @Bill Cole

      Re: B.W.There's abundant evidence to support the fact that our ancestors were fish. A couple good recent books covering this are "Why Evolution is True" and "Your Inner Fish," but there are many, at technical or beginner's levels. Go find out."

      B.C.: So your argument is based on the assumption Coyne etc is correct. Any experimental evidence?

      It is pretty clear to me that you are not prepared to engage in an earnest exchange of ideas.

      Experimental Evidence?

      Neil Shubin is uniquely positioned to juxtapose the laboratory data of Molecular Biology with field data from Paleontology! Briefly, our own genome is littered with what can best be described fossil DNA (much of it no longer functional) that can be traced back to our common ancestor to fish.

      In true Popperian fashion, Shubin and his associates can make falsifiable predictions that only be resolved in terms of common descent and NOT in terms of common (much less intelligent)design.

      The Sonic Hedgehog gene in Skate Embryo would be a case in point!

      I suggest you sit down and read Shubin’s book, especially Chapter 3.

      B.C.: Have you thought about how the genome of a fish becomes the genome of a human. What is the mechanism to get from A to Z.

      All explained by Shubin in exquisite but easily accessible to laymen – even creationist laymen.

      Again, the Sonic Hedgehog gene in Skate Embryo would be a case in point!

      I admire Shubin’s emphasis on the lack of intelligence and the lack of design abundantly obvious to any objective and disinterested observer.

      One case in point would be Shubin’s amusing elucidation of the lack of functionality for terrestrial Olfactory Genes that marine whales inherited from terrestrial ancestors.

      Delete
    22. @ Bill Cole

      I was initially hurt and disappointed to see you repeating the same falsehoods and misconceptions you expressed the last time we conversed on this blog, despite my best efforts to correct them for you.

      Then I remembered that, while with enough diligence and patience even the least gifted student will eventually learn something if sufficiently motivated, not even the best teacher in the world can educate a student who is determined to remain ignorant at all costs.

      Delete
    23. Tom Muller
      I agree with you that there is lots of biochemical connection between different species. If that is common decent then I completely agree that life is united by common biochemistry.

      Delete
    24. BW
      "So I see good reason to think evolution theory is right."
      What are the mechanisms of evolution in your opinion? i.e. the cause of the change from specie A to specie B?

      Delete
    25. lutesuite
      "I was initially hurt and disappointed to see you repeating the same falsehoods and misconceptions you expressed the last time we conversed on this blog, despite my best efforts to correct them for you."

      Sorry, but I have been highly skeptical of the positions you have taken in the past.

      Delete
    26. Like I said, if you are committed to a religious faith that requires you remain ignorant, there's not a lot anyone here can do to help you. You might as well stick with the buffoons at Uncommon Descent, where you're more at home.

      Delete
    27. BW
      My point really is simply to say that when you are arguing with someone is skeptical and you base your argument on an assumption that evolution is true, the argument appears circular to the person you are trying to convince. You tried to prove that the blood clotting system evolved by assuming that man evolved from fish. The person you are trying to convince comes from the opposite position so your argument is instantly discounted.

      Delete
    28. LS
      "Like I said, if you are committed to a religious faith that requires you remain ignorant, there's not a lot anyone here can do to help you. You might as well stick with the buffoons at Uncommon Descent, where you're more at home."
      I may have ideological bias but I am truly trying to understand the science. IMHO you are not or you would be arguing wo ad hominem attacks. You seem so sensitive to challenges to TOE it must more than science your interested in. Why don't you go to other sites where you get challenged?

      Delete
  21. Otangelo

    An exchange with you is like trying to nail Jello to the wall!

    Here is what you said earlier:

    OG So, photosynthesis is a interdependent system, that could not have evolved, since

    [1]… all parts had to be in place right from the beginning.
    [2]… It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts.


    Both contentions have been proven incorrect and you acknowledged as much

    OG You are right. If we apply the term in a strict way as coined by Behe, Photosynthesis as a whole is not irreducible complex...

    You then go back and forth as if you are again re-embracing what you already admitted to be incorrect.

    Your fallback position is then that individual components of photosynthesis (well the ETC of the Thylakoid membrane actually) are IC. The OEC in particular.

    OG In order to produce oxygen, the OEC is indispensable and irreducible, and , as i show in my study, any mutant of the proteins that constitute the OEC complex, make the function of oxygen production defective or impossible.

    This statement is blatantly false! It is wrong! I can not be kind about this: You must acknowledge as much if you want to avoid the accusation of intellectual dishonesty.

    Your rebuttal of last resort is seems to acknowledge both errors above (your indecisive waffling becomes most frustrating) but you attempt to slip through the two horns of your obvious dilemma by invoking a total misunderstanding of how evolution operates:

    OG Its irrelevant as Larry did, to claim there are simpler versions of photosynthesis. These versions do not keep the same function.

    You are arguing in circles. Larry and others are contradicting your suggestion that photosynthesis "as a whole" is Irreducibly Complex.

    That means Larry and others need to find function for bits and pieces of photosynthesis...

    ... which (drum roll please)

    ... they have successfully done!

    AND it gets better.

    Larry and others have even determined that some of these "reducible" functions were exaptations!

    But you seem to argue that exaptation is a contradiction as opposed to a validation of evolution! The expanse of your confusion is breath-taking!

    I am definitely going to build a worksheet around what you have written. I thank you for your efforts. You have made my job of defending the cogency of evolution much easier. I will share my worksheet with you when I am done.

    Thank you!

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    Replies
    1. Tom

      to your point 1. No , i have not acknowledged that oxygenic photosynthesis can operate with less than 26 enzymes and protein complexes.

      The only thing i admitted, i thought that was clear, is, that in the strict applied sense as Behe formulated what a IC system is, photosynthesis is not IC, but interdependent. Which imho in the final inference does not change anything. Namely, the origin of oxygenic photosyntesis is best explained through design.

      Then you say about my assertion that the OEC is IC: This statement is blatantly false! It is wrong! I can not be kind about this: You must acknowledge as much if you want to avoid the accusation of intellectual dishonesty.

      Neither you, nor Larry have shown why i am wrong. Try.

      In regard of your next point:

      A simpler version of oxygen producing photosynthesis would only exist, if it would keep the function of producing oxygen. Such a system DOES NOT EXIST. So Larry is simply wrong. A non oxygen producing photosynthesis pathway cannot be said to be a reduced form, if it does not keep the same function.

      Delete
  22. a parting gift for Otangelo Grasso

    Public comments by a very devout Christian on the irreducible complexity of bacterial flagella:

    http://www.millerandlevine.com/km/evol/design2/article.html

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  23. I am very grateful to Otangelo Grasso for embarking on this thread. I is obvious to me that any consideration of the Irreducible Complexity for any feature of Metabolism when promoting the notion of Intelligent Design, the very best candidate to CONTRADICT any such silliness, would in fact, be so-called “Photosynthesis”.

    I am going to cite OG’s failures in my own classroom in future and will share my efforts with my colleagues. Here is a quick précis and my first draft so far:

    1 – Various Bacterial & Archean “nonphotosynthetic photophosphorylation” systems evolved first and then later combined into the more complex process in cyanobacteria; to be inherited later by “higher plant” chloroplasts. The dual photosystems of modern chloroplasts clearly evolved late from a combination of a type I reaction center in species like Heliobacter and green sulfur bacteria and a type II reaction center from species like purple bacteria and green filamentous bacteria. The Oxygen Evolving Complex (OEC) was a later evolutionary add-on.

    These various forms of “nonphotosynthetic photophosphorylation” to generate ATP & NADPH preceded the so-called dark reactions of PGAL synthesis.

    2 - “Nonphotosynthetic photophosphorylation” still remains an important feature of chloroplasts in higher plants. For example, called “cyclic photophosphorylation” where P I generates ATP for immediate energy needs of the cell. Electrons are recycled back to P I without generating NADPH. Interestingly, the electrons transferred are not derived from water, but from P I itself, explaining why they must be recycled to P I. This version of “nonphotosynthetic photophosphorylation” does not generate Oxygen, not even in chloroplasts of higher plants. IOW, even the flowering plant photosynthesis system IS NOT irreducibly complex.

    3- Only a small percentage of the chemical energy (ATP and NADPH) produced by photosynthesis in cyanobacteria and algae is stored in carbohydrates. Much of it is used in other metabolic reactions, including protein synthesis. This is also true for so-called “higher plants”. That means that MOST of the time, so-called photosynthesis is NOT coupled to the Calvin Cycle, NOT EVEN in so-called higher “flowering plants”.

    4- The product of the Calvin cycle is glyceraldehyde-3-phosphate and not glucose, sucrose, or starch. G3P is used in all kinds of pathways such as making amino acids and nucleotides. It's not just used for storing energy by acting as a precursor to glucose and glycogen/starch. So claiming that the overall equation for photosynthesis is production of a 6-carbon sugar is misleading in more ways than one.

    5- All living cells "store energy" in the form of glycogen. This includes all those species that are incapable of photosynthesis and many that are. The role of glycogen as an energy storehouse predates photosynthesis and has nothing to do with "water photolysis."

    The fact that plants make starch instead of glycogen is irrelevant. It's a derived feature. Storage of chemical energy in the form of glucose/starch/cellulose is a later adaptation with the following advantage:
    a) The increase in the Gibbs free energy of hydrolysis due to higher concentrations of ATP (relative to ADP) would mean that spontaneous hydrolysis would become a serious problem.
    b) The big increase in the positive ΔG for synthesis of ATP would make it impossible for ATP synthetase to make any ATP against the concentration gradient.

    6- It must be emphasized that the various photophosphorylation systems that first evolved in Bacteria and Archaea do not generate oxygen by oxidative photolysis of water. As mentioned earlier, that was a later evolutionary add-on in cyanobacteria which are not very ancient relatively speaking.

    7- Introductory Biology spends a lot of time on Ecology and discussion of trophic levels. The issue becomes one of semantics where consideration of photosynthesis by “producers” to generate the “Biomass” for higher Trophic Levels can possibly lead thinking astray.

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    1. A rethink should include further consideration that

      1 – Plants can divert PGAL/G3P to other biochemical pathways other than creation of Glucose/Starch when generating “Biomass”

      2 – Plants not only can but (in fact most of the time do) decouple ATP/NADPH production from Carbon fixation. Much of the ATP & NADPH generated by Photosystems II & I respectively are in fact redirected to immediate energy needs, even in flowering plants.

      IOW, some persistent fuzziness in thinking is in small part due to a conflation of photosynthesis with generation of Biomass which itself becomes conflated with generation of Glucose/Starch/Cellulose

      The events occurring in the inner membrane are NOT “irreducibly complex” and can be basically broken down into two complementary events:

      1 - events leading to the generation of useful ATP (photosystem II) and

      2 - events leading to the generation of useful NADP (photosystem I)

      3 – events leading to the OEC

      Continuing on the subject of Complex Irreducibility, both photosystems employ Porphyrins and Carotenoids which are important in various metabolic processes(not just photosynthesis) meaning their evolutionary history may reflect many other functions only to be co-opted later for photosynthesis. Meanwhile both can be demonstrated to have abiogenic origins.
      In other words, so-called photosynthesis “as a whole” is not Irreducibly Complex. Is it possible that individual components are uniquely irreducibly complex? Three possible candidates would be P II, ATP Synthase, and OEC.
      -ATP Synthase has commonalities with a DNA helicase with ATPase activity and H+ motors of Flagella
      - the OEC resembles two catalase enzymes lashed together whose exaptation was protection of the cell from the problems peroxide resulting from anaerobic metabolism
      - P II can be shown to have evolved in stepwise modular fashion.
      Finally, Light-driven proton pumps emerged as an evolutionary afterthought (as it were) to do the job of alkaline vents as described in Nick Lane’s book describing the chemo-osmotic origins of life.

      These light sensitive proteins were then co-opted to evolve sensory receptors important in bacterial phototaxis. These same proteins were then subsequently co-opted in the convergent evolution of eyes.

      Essentially, we are all seeing with bacterial eyes. Meaning even the favored shibboleth of Creationists the complex eye is irreducibly complex
      In summary, much of what Creationists deem Irreducibly Complex in fact are reducible exaltations of exaptations validating evolution.

      How is that for a hasty first draft?

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